From 3f75f35d1a14601f26a53e13b913a7b67415c7db Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 14:19:40 +0100 Subject: [PATCH 01/14] :truck: move nf-core modules in nf-core folder --- modules/{cnr-ibba => nf-core}/bcftools/concat/main.nf | 0 modules/{cnr-ibba => nf-core}/bcftools/concat/meta.yml | 0 modules/{cnr-ibba => nf-core}/samtools/coverage/main.nf | 0 modules/{cnr-ibba => nf-core}/samtools/coverage/meta.yml | 0 modules/{cnr-ibba => nf-core}/samtools/flagstat/main.nf | 0 modules/{cnr-ibba => nf-core}/samtools/flagstat/meta.yml | 0 modules/{cnr-ibba => nf-core}/samtools/idxstats/main.nf | 0 modules/{cnr-ibba => nf-core}/samtools/idxstats/meta.yml | 0 modules/{cnr-ibba => nf-core}/samtools/stats/main.nf | 0 modules/{cnr-ibba => nf-core}/samtools/stats/meta.yml | 0 modules/{cnr-ibba => nf-core}/tabix/tabix/main.nf | 0 modules/{cnr-ibba => nf-core}/tabix/tabix/meta.yml | 0 subworkflows/cnr-ibba/freebayes_parallel/main.nf | 4 ++-- .../{cnr-ibba => nf-core}/bam_stats_samtools/main.nf | 6 +++--- .../{cnr-ibba => nf-core}/bam_stats_samtools/meta.yml | 0 .../modules/{cnr-ibba => nf-core}/bcftools/concat/main.nf | 2 +- .../{cnr-ibba => nf-core}/bcftools/concat/nextflow.config | 0 .../{cnr-ibba => nf-core}/bcftools/concat/test.yml | 0 .../{cnr-ibba => nf-core}/samtools/coverage/main.nf | 0 .../samtools/coverage/nextflow.config | 0 .../{cnr-ibba => nf-core}/samtools/coverage/test.yml | 0 .../{cnr-ibba => nf-core}/samtools/flagstat/main.nf | 2 +- .../samtools/flagstat/nextflow.config | 0 .../{cnr-ibba => nf-core}/samtools/flagstat/test.yml | 0 .../{cnr-ibba => nf-core}/samtools/idxstats/main.nf | 2 +- .../samtools/idxstats/nextflow.config | 0 .../{cnr-ibba => nf-core}/samtools/idxstats/test.yml | 0 .../modules/{cnr-ibba => nf-core}/samtools/stats/main.nf | 2 +- .../{cnr-ibba => nf-core}/samtools/stats/nextflow.config | 0 .../modules/{cnr-ibba => nf-core}/samtools/stats/test.yml | 0 tests/modules/{cnr-ibba => nf-core}/tabix/tabix/main.nf | 8 ++++---- .../{cnr-ibba => nf-core}/tabix/tabix/nextflow.config | 0 tests/modules/{cnr-ibba => nf-core}/tabix/tabix/test.yml | 0 33 files changed, 13 insertions(+), 13 deletions(-) rename modules/{cnr-ibba => nf-core}/bcftools/concat/main.nf (100%) rename modules/{cnr-ibba => nf-core}/bcftools/concat/meta.yml (100%) rename modules/{cnr-ibba => nf-core}/samtools/coverage/main.nf (100%) rename modules/{cnr-ibba => nf-core}/samtools/coverage/meta.yml (100%) rename modules/{cnr-ibba => nf-core}/samtools/flagstat/main.nf (100%) rename modules/{cnr-ibba => nf-core}/samtools/flagstat/meta.yml (100%) rename modules/{cnr-ibba => nf-core}/samtools/idxstats/main.nf (100%) rename modules/{cnr-ibba => nf-core}/samtools/idxstats/meta.yml (100%) rename modules/{cnr-ibba => nf-core}/samtools/stats/main.nf (100%) rename modules/{cnr-ibba => nf-core}/samtools/stats/meta.yml (100%) rename modules/{cnr-ibba => nf-core}/tabix/tabix/main.nf (100%) rename modules/{cnr-ibba => nf-core}/tabix/tabix/meta.yml (100%) rename subworkflows/{cnr-ibba => nf-core}/bam_stats_samtools/main.nf (77%) rename subworkflows/{cnr-ibba => nf-core}/bam_stats_samtools/meta.yml (100%) rename tests/modules/{cnr-ibba => nf-core}/bcftools/concat/main.nf (91%) rename tests/modules/{cnr-ibba => nf-core}/bcftools/concat/nextflow.config (100%) rename tests/modules/{cnr-ibba => nf-core}/bcftools/concat/test.yml (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/coverage/main.nf (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/coverage/nextflow.config (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/coverage/test.yml (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/flagstat/main.nf (81%) rename tests/modules/{cnr-ibba => nf-core}/samtools/flagstat/nextflow.config (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/flagstat/test.yml (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/idxstats/main.nf (81%) rename tests/modules/{cnr-ibba => nf-core}/samtools/idxstats/nextflow.config (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/idxstats/test.yml (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/stats/main.nf (91%) rename tests/modules/{cnr-ibba => nf-core}/samtools/stats/nextflow.config (100%) rename tests/modules/{cnr-ibba => nf-core}/samtools/stats/test.yml (100%) rename tests/modules/{cnr-ibba => nf-core}/tabix/tabix/main.nf (89%) rename tests/modules/{cnr-ibba => nf-core}/tabix/tabix/nextflow.config (100%) rename tests/modules/{cnr-ibba => nf-core}/tabix/tabix/test.yml (100%) diff --git a/modules/cnr-ibba/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf similarity index 100% rename from modules/cnr-ibba/bcftools/concat/main.nf rename to modules/nf-core/bcftools/concat/main.nf diff --git a/modules/cnr-ibba/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml similarity index 100% rename from modules/cnr-ibba/bcftools/concat/meta.yml rename to modules/nf-core/bcftools/concat/meta.yml diff --git a/modules/cnr-ibba/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf similarity index 100% rename from modules/cnr-ibba/samtools/coverage/main.nf rename to modules/nf-core/samtools/coverage/main.nf diff --git a/modules/cnr-ibba/samtools/coverage/meta.yml b/modules/nf-core/samtools/coverage/meta.yml similarity index 100% rename from modules/cnr-ibba/samtools/coverage/meta.yml rename to modules/nf-core/samtools/coverage/meta.yml diff --git a/modules/cnr-ibba/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf similarity index 100% rename from modules/cnr-ibba/samtools/flagstat/main.nf rename to modules/nf-core/samtools/flagstat/main.nf diff --git a/modules/cnr-ibba/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml similarity index 100% rename from modules/cnr-ibba/samtools/flagstat/meta.yml rename to modules/nf-core/samtools/flagstat/meta.yml diff --git a/modules/cnr-ibba/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf similarity index 100% rename from modules/cnr-ibba/samtools/idxstats/main.nf rename to modules/nf-core/samtools/idxstats/main.nf diff --git a/modules/cnr-ibba/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml similarity index 100% rename from modules/cnr-ibba/samtools/idxstats/meta.yml rename to modules/nf-core/samtools/idxstats/meta.yml diff --git a/modules/cnr-ibba/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf similarity index 100% rename from modules/cnr-ibba/samtools/stats/main.nf rename to modules/nf-core/samtools/stats/main.nf diff --git a/modules/cnr-ibba/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml similarity index 100% rename from modules/cnr-ibba/samtools/stats/meta.yml rename to modules/nf-core/samtools/stats/meta.yml diff --git a/modules/cnr-ibba/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf similarity index 100% rename from modules/cnr-ibba/tabix/tabix/main.nf rename to modules/nf-core/tabix/tabix/main.nf diff --git a/modules/cnr-ibba/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml similarity index 100% rename from modules/cnr-ibba/tabix/tabix/meta.yml rename to modules/nf-core/tabix/tabix/meta.yml diff --git a/subworkflows/cnr-ibba/freebayes_parallel/main.nf b/subworkflows/cnr-ibba/freebayes_parallel/main.nf index 90acf77..adb2064 100644 --- a/subworkflows/cnr-ibba/freebayes_parallel/main.nf +++ b/subworkflows/cnr-ibba/freebayes_parallel/main.nf @@ -4,8 +4,8 @@ include { FREEBAYES_SPLITBAM } from '../../../modules/cnr-ibba/freebayes/splitbam/main' include { FREEBAYES_CHUNK } from '../../../modules/cnr-ibba/freebayes/chunk/main' -include { BCFTOOLS_CONCAT as FREEBAYES_CONCAT } from '../../../modules/cnr-ibba/bcftools/concat/main' -include { TABIX_TABIX as FREEBAYES_TABIX } from '../../../modules/cnr-ibba/tabix/tabix/main' +include { BCFTOOLS_CONCAT as FREEBAYES_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' +include { TABIX_TABIX as FREEBAYES_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow FREEBAYES_PARALLEL { take: diff --git a/subworkflows/cnr-ibba/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf similarity index 77% rename from subworkflows/cnr-ibba/bam_stats_samtools/main.nf rename to subworkflows/nf-core/bam_stats_samtools/main.nf index cdc02d3..cfcc48d 100644 --- a/subworkflows/cnr-ibba/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -2,9 +2,9 @@ // Run SAMtools stats, flagstat and idxstats // -include { SAMTOOLS_STATS } from '../../../modules/cnr-ibba/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../../modules/cnr-ibba/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/cnr-ibba/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' workflow BAM_STATS_SAMTOOLS { take: diff --git a/subworkflows/cnr-ibba/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml similarity index 100% rename from subworkflows/cnr-ibba/bam_stats_samtools/meta.yml rename to subworkflows/nf-core/bam_stats_samtools/meta.yml diff --git a/tests/modules/cnr-ibba/bcftools/concat/main.nf b/tests/modules/nf-core/bcftools/concat/main.nf similarity index 91% rename from tests/modules/cnr-ibba/bcftools/concat/main.nf rename to tests/modules/nf-core/bcftools/concat/main.nf index 2f851d8..5ff032f 100644 --- a/tests/modules/cnr-ibba/bcftools/concat/main.nf +++ b/tests/modules/nf-core/bcftools/concat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONCAT } from '../../../../../modules/cnr-ibba/bcftools/concat/main.nf' +include { BCFTOOLS_CONCAT } from '../../../../../modules/nf-core/bcftools/concat/main.nf' workflow test_bcftools_concat_tbi { diff --git a/tests/modules/cnr-ibba/bcftools/concat/nextflow.config b/tests/modules/nf-core/bcftools/concat/nextflow.config similarity index 100% rename from tests/modules/cnr-ibba/bcftools/concat/nextflow.config rename to tests/modules/nf-core/bcftools/concat/nextflow.config diff --git a/tests/modules/cnr-ibba/bcftools/concat/test.yml b/tests/modules/nf-core/bcftools/concat/test.yml similarity index 100% rename from tests/modules/cnr-ibba/bcftools/concat/test.yml rename to tests/modules/nf-core/bcftools/concat/test.yml diff --git a/tests/modules/cnr-ibba/samtools/coverage/main.nf b/tests/modules/nf-core/samtools/coverage/main.nf similarity index 100% rename from tests/modules/cnr-ibba/samtools/coverage/main.nf rename to tests/modules/nf-core/samtools/coverage/main.nf diff --git a/tests/modules/cnr-ibba/samtools/coverage/nextflow.config b/tests/modules/nf-core/samtools/coverage/nextflow.config similarity index 100% rename from tests/modules/cnr-ibba/samtools/coverage/nextflow.config rename to tests/modules/nf-core/samtools/coverage/nextflow.config diff --git a/tests/modules/cnr-ibba/samtools/coverage/test.yml b/tests/modules/nf-core/samtools/coverage/test.yml similarity index 100% rename from tests/modules/cnr-ibba/samtools/coverage/test.yml rename to tests/modules/nf-core/samtools/coverage/test.yml diff --git a/tests/modules/cnr-ibba/samtools/flagstat/main.nf b/tests/modules/nf-core/samtools/flagstat/main.nf similarity index 81% rename from tests/modules/cnr-ibba/samtools/flagstat/main.nf rename to tests/modules/nf-core/samtools/flagstat/main.nf index 4dc6d56..c1a435f 100644 --- a/tests/modules/cnr-ibba/samtools/flagstat/main.nf +++ b/tests/modules/nf-core/samtools/flagstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FLAGSTAT } from '../../../../../modules/cnr-ibba/samtools/flagstat/main.nf' +include { SAMTOOLS_FLAGSTAT } from '../../../../../modules/nf-core/samtools/flagstat/main.nf' workflow test_samtools_flagstat { input = [ diff --git a/tests/modules/cnr-ibba/samtools/flagstat/nextflow.config b/tests/modules/nf-core/samtools/flagstat/nextflow.config similarity index 100% rename from tests/modules/cnr-ibba/samtools/flagstat/nextflow.config rename to tests/modules/nf-core/samtools/flagstat/nextflow.config diff --git a/tests/modules/cnr-ibba/samtools/flagstat/test.yml b/tests/modules/nf-core/samtools/flagstat/test.yml similarity index 100% rename from tests/modules/cnr-ibba/samtools/flagstat/test.yml rename to tests/modules/nf-core/samtools/flagstat/test.yml diff --git a/tests/modules/cnr-ibba/samtools/idxstats/main.nf b/tests/modules/nf-core/samtools/idxstats/main.nf similarity index 81% rename from tests/modules/cnr-ibba/samtools/idxstats/main.nf rename to tests/modules/nf-core/samtools/idxstats/main.nf index 34d4804..4a29252 100644 --- a/tests/modules/cnr-ibba/samtools/idxstats/main.nf +++ b/tests/modules/nf-core/samtools/idxstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_IDXSTATS } from '../../../../../modules/cnr-ibba/samtools/idxstats/main.nf' +include { SAMTOOLS_IDXSTATS } from '../../../../../modules/nf-core/samtools/idxstats/main.nf' workflow test_samtools_idxstats { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/cnr-ibba/samtools/idxstats/nextflow.config b/tests/modules/nf-core/samtools/idxstats/nextflow.config similarity index 100% rename from tests/modules/cnr-ibba/samtools/idxstats/nextflow.config rename to tests/modules/nf-core/samtools/idxstats/nextflow.config diff --git a/tests/modules/cnr-ibba/samtools/idxstats/test.yml b/tests/modules/nf-core/samtools/idxstats/test.yml similarity index 100% rename from tests/modules/cnr-ibba/samtools/idxstats/test.yml rename to tests/modules/nf-core/samtools/idxstats/test.yml diff --git a/tests/modules/cnr-ibba/samtools/stats/main.nf b/tests/modules/nf-core/samtools/stats/main.nf similarity index 91% rename from tests/modules/cnr-ibba/samtools/stats/main.nf rename to tests/modules/nf-core/samtools/stats/main.nf index 6131244..523056a 100644 --- a/tests/modules/cnr-ibba/samtools/stats/main.nf +++ b/tests/modules/nf-core/samtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_STATS } from '../../../../../modules/cnr-ibba/samtools/stats/main.nf' +include { SAMTOOLS_STATS } from '../../../../../modules/nf-core/samtools/stats/main.nf' workflow test_samtools_stats { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/cnr-ibba/samtools/stats/nextflow.config b/tests/modules/nf-core/samtools/stats/nextflow.config similarity index 100% rename from tests/modules/cnr-ibba/samtools/stats/nextflow.config rename to tests/modules/nf-core/samtools/stats/nextflow.config diff --git a/tests/modules/cnr-ibba/samtools/stats/test.yml b/tests/modules/nf-core/samtools/stats/test.yml similarity index 100% rename from tests/modules/cnr-ibba/samtools/stats/test.yml rename to tests/modules/nf-core/samtools/stats/test.yml diff --git a/tests/modules/cnr-ibba/tabix/tabix/main.nf b/tests/modules/nf-core/tabix/tabix/main.nf similarity index 89% rename from tests/modules/cnr-ibba/tabix/tabix/main.nf rename to tests/modules/nf-core/tabix/tabix/main.nf index ad2c57d..31b78e0 100644 --- a/tests/modules/cnr-ibba/tabix/tabix/main.nf +++ b/tests/modules/nf-core/tabix/tabix/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -include { TABIX_TABIX as TABIX_BED } from '../../../../../modules/cnr-ibba/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_GFF } from '../../../../../modules/cnr-ibba/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../../modules/cnr-ibba/tabix/tabix/main.nf' -include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../../modules/cnr-ibba/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_BED } from '../../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_GFF } from '../../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../../modules/nf-core/tabix/tabix/main.nf' +include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../../modules/nf-core/tabix/tabix/main.nf' workflow test_tabix_tabix_bed { input = [ [ id:'B.bed' ], // meta map diff --git a/tests/modules/cnr-ibba/tabix/tabix/nextflow.config b/tests/modules/nf-core/tabix/tabix/nextflow.config similarity index 100% rename from tests/modules/cnr-ibba/tabix/tabix/nextflow.config rename to tests/modules/nf-core/tabix/tabix/nextflow.config diff --git a/tests/modules/cnr-ibba/tabix/tabix/test.yml b/tests/modules/nf-core/tabix/tabix/test.yml similarity index 100% rename from tests/modules/cnr-ibba/tabix/tabix/test.yml rename to tests/modules/nf-core/tabix/tabix/test.yml From 3aed8e0883e40e7db422803d891532c2d08b5561 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 14:39:53 +0100 Subject: [PATCH 02/14] :fire: remove and fix tests configurations --- tests/config/pytest_modules.yml | 2888 +------------------------------ 1 file changed, 19 insertions(+), 2869 deletions(-) diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e1bf361..e6431fc 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,943 +1,14 @@ -abacas: - - modules/cnr-ibba/abacas/** - - tests/modules/cnr-ibba/abacas/** - -abricate/run: - - modules/cnr-ibba/abricate/run/** - - tests/modules/cnr-ibba/abricate/run/** - -abricate/summary: - - modules/cnr-ibba/abricate/summary/** - - tests/modules/cnr-ibba/abricate/summary/** - -adapterremoval: - - modules/cnr-ibba/adapterremoval/** - - tests/modules/cnr-ibba/adapterremoval/** - -adapterremovalfixprefix: - - modules/cnr-ibba/adapterremovalfixprefix/** - - tests/modules/cnr-ibba/adapterremovalfixprefix/** - -agrvate: - - modules/cnr-ibba/agrvate/** - - tests/modules/cnr-ibba/agrvate/** - -allelecounter: - - modules/cnr-ibba/allelecounter/** - - tests/modules/cnr-ibba/allelecounter/** - -ampir: - - modules/cnr-ibba/ampir/** - - tests/modules/cnr-ibba/ampir/** - -amplify/predict: - - modules/cnr-ibba/amplify/predict/** - - tests/modules/cnr-ibba/amplify/predict/** - -amps: - - modules/cnr-ibba/amps/** - - tests/modules/cnr-ibba/amps/** - -amrfinderplus/run: - - modules/cnr-ibba/amrfinderplus/run/** - - tests/modules/cnr-ibba/amrfinderplus/run/** - -amrfinderplus/update: - - modules/cnr-ibba/amrfinderplus/update/** - - tests/modules/cnr-ibba/amrfinderplus/update/** - -angsd/docounts: - - modules/cnr-ibba/angsd/docounts/** - - tests/modules/cnr-ibba/angsd/docounts/** - -antismash/antismashlite: - - modules/cnr-ibba/antismash/antismashlite/** - - tests/modules/cnr-ibba/antismash/antismashlite/** - -antismash/antismashlitedownloaddatabases: - - modules/cnr-ibba/antismash/antismashlitedownloaddatabases/** - - tests/modules/cnr-ibba/antismash/antismashlitedownloaddatabases/** - -aria2: - - modules/cnr-ibba/aria2/** - - tests/modules/cnr-ibba/aria2/** - -ariba/getref: - - modules/cnr-ibba/ariba/getref/** - - tests/modules/cnr-ibba/ariba/getref/** - -ariba/run: - - modules/cnr-ibba/ariba/run/** - - tests/modules/cnr-ibba/ariba/run/** - -arriba: - - modules/cnr-ibba/arriba/** - - tests/modules/cnr-ibba/arriba/** - -artic/guppyplex: - - modules/cnr-ibba/artic/guppyplex/** - - tests/modules/cnr-ibba/artic/guppyplex/** - -artic/minion: - - modules/cnr-ibba/artic/minion/** - - tests/modules/cnr-ibba/artic/minion/** - -ascat: - - modules/cnr-ibba/ascat/** - - tests/modules/cnr-ibba/ascat/** - -assemblyscan: - - modules/cnr-ibba/assemblyscan/** - - tests/modules/cnr-ibba/assemblyscan/** - -ataqv/ataqv: - - modules/cnr-ibba/ataqv/ataqv/** - - tests/modules/cnr-ibba/ataqv/ataqv/** - -ataqv/mkarv: - - modules/cnr-ibba/ataqv/mkarv/** - - tests/modules/cnr-ibba/ataqv/mkarv/** - -atlas/call: - - modules/cnr-ibba/atlas/call/** - - tests/modules/cnr-ibba/atlas/call/** - -atlas/pmd: - - modules/cnr-ibba/atlas/pmd/** - - tests/modules/cnr-ibba/atlas/pmd/** - -atlas/recal: - - modules/cnr-ibba/atlas/recal/** - - tests/modules/cnr-ibba/atlas/recal/** - -atlas/splitmerge: - - modules/cnr-ibba/atlas/splitmerge/** - - tests/modules/cnr-ibba/atlas/splitmerge/** - -atlasgeneannotationmanipulation/gtf2featureannotation: - - modules/cnr-ibba/atlasgeneannotationmanipulation/gtf2featureannotation/** - - tests/modules/cnr-ibba/atlasgeneannotationmanipulation/gtf2featureannotation/** - -bakta: - - modules/cnr-ibba/bakta/** - - tests/modules/cnr-ibba/bakta/** - bamaddrg: - modules/cnr-ibba/bamaddrg/** - tests/modules/cnr-ibba/bamaddrg/** -bamaligncleaner: - - modules/cnr-ibba/bamaligncleaner/** - - tests/modules/cnr-ibba/bamaligncleaner/** - -bamcmp: - - modules/cnr-ibba/bamcmp/** - - tests/modules/cnr-ibba/bamcmp/** - -bamtools/convert: - - modules/cnr-ibba/bamtools/convert/** - - tests/modules/cnr-ibba/bamtools/convert/** - bamtools/coverage: - modules/cnr-ibba/bamtools/coverage/** - tests/modules/cnr-ibba/bamtools/coverage/** -bamtools/split: - - modules/cnr-ibba/bamtools/split/** - - tests/modules/cnr-ibba/bamtools/split/** - -bamtools/stats: - - modules/cnr-ibba/bamtools/stats/** - - tests/modules/cnr-ibba/bamtools/stats/** - -bamutil/trimbam: - - modules/cnr-ibba/bamutil/trimbam/** - - tests/modules/cnr-ibba/bamutil/trimbam/** - -bandage/image: - - modules/cnr-ibba/bandage/image/** - - tests/modules/cnr-ibba/bandage/image/** - -bases2fastq: - - modules/cnr-ibba/bases2fastq/** - - tests/modules/cnr-ibba/bases2fastq/** - -bbmap/align: - - modules/cnr-ibba/bbmap/align/** - - tests/modules/cnr-ibba/bbmap/align/** - -bbmap/bbduk: - - modules/cnr-ibba/bbmap/bbduk/** - - tests/modules/cnr-ibba/bbmap/bbduk/** - -bbmap/bbsplit: - - modules/cnr-ibba/bbmap/bbsplit/** - - tests/modules/cnr-ibba/bbmap/bbsplit/** - -bbmap/clumpify: - - modules/cnr-ibba/bbmap/clumpify/** - - tests/modules/cnr-ibba/bbmap/clumpify/** - -bbmap/index: - - modules/cnr-ibba/bbmap/index/** - - tests/modules/cnr-ibba/bbmap/index/** - -bbmap/pileup: - - modules/cnr-ibba/bbmap/pileup/** - - tests/modules/cnr-ibba/bbmap/pileup/** - -bcftools/annotate: - - modules/cnr-ibba/bcftools/annotate/** - - tests/modules/cnr-ibba/bcftools/annotate/** - bcftools/concat: - - modules/cnr-ibba/bcftools/concat/** - - tests/modules/cnr-ibba/bcftools/concat/** - -bcftools/consensus: - - modules/cnr-ibba/bcftools/consensus/** - - tests/modules/cnr-ibba/bcftools/consensus/** - -bcftools/convert: - - modules/cnr-ibba/bcftools/convert/** - - tests/modules/cnr-ibba/bcftools/convert/** - -bcftools/filter: - - modules/cnr-ibba/bcftools/filter/** - - tests/modules/cnr-ibba/bcftools/filter/** - -bcftools/index: - - modules/cnr-ibba/bcftools/index/** - - tests/modules/cnr-ibba/bcftools/index** - -bcftools/isec: - - modules/cnr-ibba/bcftools/isec/** - - tests/modules/cnr-ibba/bcftools/isec/** - -bcftools/merge: - - modules/cnr-ibba/bcftools/merge/** - - tests/modules/cnr-ibba/bcftools/merge/** - -bcftools/mpileup: - - modules/cnr-ibba/bcftools/mpileup/** - - tests/modules/cnr-ibba/bcftools/mpileup/** - -bcftools/norm: - - modules/cnr-ibba/bcftools/norm/** - - tests/modules/cnr-ibba/bcftools/norm/** - -bcftools/query: - - modules/cnr-ibba/bcftools/query/** - - tests/modules/cnr-ibba/bcftools/query/** - -bcftools/reheader: - - modules/cnr-ibba/bcftools/reheader/** - - tests/modules/cnr-ibba/bcftools/reheader/** - -bcftools/roh: - - modules/cnr-ibba/bcftools/roh/** - - tests/modules/cnr-ibba/bcftools/roh/** - -bcftools/sort: - - modules/cnr-ibba/bcftools/sort/** - - tests/modules/cnr-ibba/bcftools/sort/** - -bcftools/stats: - - modules/cnr-ibba/bcftools/stats/** - - tests/modules/cnr-ibba/bcftools/stats/** - -bcftools/view: - - modules/cnr-ibba/bcftools/view/** - - tests/modules/cnr-ibba/bcftools/view/** - -bcl2fastq: - - modules/cnr-ibba/bcl2fastq/** - - tests/modules/cnr-ibba/bcl2fastq/** - -bclconvert: - - modules/cnr-ibba/bclconvert/** - - tests/modules/cnr-ibba/bclconvert/** - -bedtools/bamtobed: - - modules/cnr-ibba/bedtools/bamtobed/** - - tests/modules/cnr-ibba/bedtools/bamtobed/** - -bedtools/closest: - - modules/cnr-ibba/bedtools/closest/** - - tests/modules/cnr-ibba/bedtools/closest/** - -bedtools/complement: - - modules/cnr-ibba/bedtools/complement/** - - tests/modules/cnr-ibba/bedtools/complement/** - -bedtools/coverage: - - modules/cnr-ibba/bedtools/coverage/** - - tests/modules/cnr-ibba/bedtools/coverage/** - -bedtools/genomecov: - - modules/cnr-ibba/bedtools/genomecov/** - - tests/modules/cnr-ibba/bedtools/genomecov/** - -bedtools/getfasta: - - modules/cnr-ibba/bedtools/getfasta/** - - tests/modules/cnr-ibba/bedtools/getfasta/** - -bedtools/intersect: - - modules/cnr-ibba/bedtools/intersect/** - - tests/modules/cnr-ibba/bedtools/intersect/** - -bedtools/makewindows: - - modules/cnr-ibba/bedtools/makewindows/** - - tests/modules/cnr-ibba/bedtools/makewindows/** - -bedtools/maskfasta: - - modules/cnr-ibba/bedtools/maskfasta/** - - tests/modules/cnr-ibba/bedtools/maskfasta/** - -bedtools/merge: - - modules/cnr-ibba/bedtools/merge/** - - tests/modules/cnr-ibba/bedtools/merge/** - -bedtools/slop: - - modules/cnr-ibba/bedtools/slop/** - - tests/modules/cnr-ibba/bedtools/slop/** - -bedtools/sort: - - modules/cnr-ibba/bedtools/sort/** - - tests/modules/cnr-ibba/bedtools/sort/** - -bedtools/split: - - modules/cnr-ibba/bedtools/split/** - - tests/modules/cnr-ibba/bedtools/split/** - -bedtools/subtract: - - modules/cnr-ibba/bedtools/subtract/** - - tests/modules/cnr-ibba/bedtools/subtract/** - -biobambam/bammarkduplicates2: - - modules/cnr-ibba/biobambam/bammarkduplicates2/** - - tests/modules/cnr-ibba/biobambam/bammarkduplicates2/** - -biobambam/bammerge: - - modules/cnr-ibba/biobambam/bammerge/** - - tests/modules/cnr-ibba/biobambam/bammerge/** - -biobambam/bamsormadup: - - modules/cnr-ibba/biobambam/bamsormadup/** - - tests/modules/cnr-ibba/biobambam/bamsormadup/** - -biohansel: - - modules/cnr-ibba/biohansel/** - - tests/modules/cnr-ibba/biohansel/** - -biscuit/align: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/align/** - - tests/modules/cnr-ibba/biscuit/align/** - -biscuit/biscuitblaster: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/biscuitblaster/** - - tests/modules/cnr-ibba/biscuit/biscuitblaster/** - -biscuit/bsconv: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/bsconv/** - - tests/modules/cnr-ibba/biscuit/bsconv/** - -biscuit/epiread: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/epiread/** - - tests/modules/cnr-ibba/biscuit/epiread/** - -biscuit/index: - - modules/cnr-ibba/biscuit/index/** - - tests/modules/cnr-ibba/biscuit/index/** - -biscuit/mergecg: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/mergecg/** - - tests/modules/cnr-ibba/biscuit/mergecg/** - -biscuit/pileup: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/pileup/** - - tests/modules/cnr-ibba/biscuit/pileup/** - -biscuit/qc: - - modules/cnr-ibba/biscuit/index/** - - modules/cnr-ibba/biscuit/qc/** - - tests/modules/cnr-ibba/biscuit/qc/** - -biscuit/vcf2bed: - - modules/cnr-ibba/biscuit/vcf2bed/** - - tests/modules/cnr-ibba/biscuit/vcf2bed/** - -bismark/align: - - modules/cnr-ibba/bismark/align/** - - modules/cnr-ibba/bismark/genomepreparation/** - - tests/modules/cnr-ibba/bismark/align/** - -bismark/deduplicate: - - modules/cnr-ibba/bismark/deduplicate/** - - tests/modules/cnr-ibba/bismark/deduplicate/** - -bismark/genomepreparation: - - modules/cnr-ibba/bismark/genomepreparation/** - - tests/modules/cnr-ibba/bismark/genomepreparation/** - -bismark/methylationextractor: - - modules/cnr-ibba/bismark/methylationextractor/** - - modules/cnr-ibba/bismark/genomepreparation/** - - tests/modules/cnr-ibba/bismark/methylationextractor/** - -bismark/report: - - modules/cnr-ibba/bismark/genomepreparation/** - - modules/cnr-ibba/bismark/align/** - - modules/cnr-ibba/bismark/deduplicate/** - - modules/cnr-ibba/bismark/methylationextractor/** - - modules/cnr-ibba/bismark/report/** - - tests/modules/cnr-ibba/bismark/report/** - -bismark/summary: - - modules/cnr-ibba/bismark/genomepreparation/** - - modules/cnr-ibba/bismark/align/** - - modules/cnr-ibba/bismark/deduplicate/** - - modules/cnr-ibba/bismark/methylationextractor/** - - modules/cnr-ibba/bismark/summary/** - - tests/modules/cnr-ibba/bismark/summary/** - -blast/blastn: - - modules/cnr-ibba/blast/blastn/** - - tests/modules/cnr-ibba/blast/blastn/** - -blast/makeblastdb: - - modules/cnr-ibba/blast/makeblastdb/** - - tests/modules/cnr-ibba/blast/makeblastdb/** - -blast/tblastn: - - modules/cnr-ibba/blast/tblastn/** - - tests/modules/cnr-ibba/blast/tblastn/** - -bowtie/align: - - modules/cnr-ibba/bowtie/align/** - - modules/cnr-ibba/bowtie/build/** - - tests/modules/cnr-ibba/bowtie/align/** - -bowtie/build: - - modules/cnr-ibba/bowtie/build/** - - tests/modules/cnr-ibba/bowtie/build_test/** - -bowtie2/align: - - modules/cnr-ibba/bowtie2/align/** - - modules/cnr-ibba/bowtie2/build/** - - tests/modules/cnr-ibba/bowtie2/align/** - -bowtie2/build: - - modules/cnr-ibba/bowtie2/build/** - - tests/modules/cnr-ibba/bowtie2/build_test/** - -bracken/bracken: - - modules/cnr-ibba/bracken/bracken/** - - tests/modules/cnr-ibba/bracken/bracken/** - -bracken/combinebrackenoutputs: - - modules/cnr-ibba/bracken/combinebrackenoutputs/** - - tests/modules/cnr-ibba/bracken/combinebrackenoutputs/** - -busco: - - modules/cnr-ibba/busco/** - - tests/modules/cnr-ibba/busco/** - -bwa/aln: - - modules/cnr-ibba/bwa/aln/** - - tests/modules/cnr-ibba/bwa/aln/** - -bwa/index: - - modules/cnr-ibba/bwa/index/** - - tests/modules/cnr-ibba/bwa/index/** - -bwa/mem: - - modules/cnr-ibba/bwa/mem/** - - tests/modules/cnr-ibba/bwa/mem/** - -bwa/sampe: - - modules/cnr-ibba/bwa/sampe/** - - tests/modules/cnr-ibba/bwa/sampe/** - -bwa/samse: - - modules/cnr-ibba/bwa/samse/** - - tests/modules/cnr-ibba/bwa/samse/** - -bwamem2/index: - - modules/cnr-ibba/bwamem2/index/** - - tests/modules/cnr-ibba/bwamem2/index/** - -bwamem2/mem: - - modules/cnr-ibba/bwamem2/mem/** - - tests/modules/cnr-ibba/bwamem2/mem/** - -bwameth/align: - - modules/cnr-ibba/bwameth/align/** - - tests/modules/cnr-ibba/bwameth/align/** - -bwameth/index: - - modules/cnr-ibba/bwameth/index/** - - tests/modules/cnr-ibba/bwameth/index/** - -calder2: - - modules/cnr-ibba/calder2/** - - tests/modules/cnr-ibba/calder2/** - -cat/cat: - - modules/cnr-ibba/cat/cat/** - - tests/modules/cnr-ibba/cat/cat/** - -cat/fastq: - - modules/cnr-ibba/cat/fastq/** - - tests/modules/cnr-ibba/cat/fastq/** - -cellranger/count: - - modules/cnr-ibba/cellranger/count/** - - tests/modules/cnr-ibba/cellranger/count/** - - modules/cnr-ibba/cellranger/mkref/** - - tests/modules/cnr-ibba/cellranger/mkref/** - - modules/cnr-ibba/cellranger/gtf/** - - tests/modules/cnr-ibba/cellranger/gtf/** - -cellranger/gtf: - - modules/cnr-ibba/cellranger/gtf/** - - tests/modules/cnr-ibba/cellranger/gtf/** - -cellranger/mkfastq: - - modules/cnr-ibba/cellranger/mkfastq/** - - tests/modules/cnr-ibba/cellranger/mkfastq/** - -cellranger/mkgtf: - - modules/cnr-ibba/cellranger/mkgtf/** - - tests/modules/cnr-ibba/cellranger/mkgtf/** - -cellranger/mkref: - - modules/cnr-ibba/cellranger/mkref/** - - tests/modules/cnr-ibba/cellranger/mkref/** - - modules/cnr-ibba/cellranger/gtf/** - - tests/modules/cnr-ibba/cellranger/gtf/** - -centrifuge/centrifuge: - - modules/cnr-ibba/centrifuge/centrifuge/** - - tests/modules/cnr-ibba/centrifuge/centrifuge/** - -checkm/lineagewf: - - modules/cnr-ibba/checkm/lineagewf/** - - tests/modules/cnr-ibba/checkm/lineagewf/** - -checkm/qa: - - modules/cnr-ibba/checkm/qa/** - - tests/modules/cnr-ibba/checkm/qa/** - -chromap/chromap: - - modules/cnr-ibba/chromap/chromap/** - - tests/modules/cnr-ibba/chromap/chromap/** - -chromap/index: - - modules/cnr-ibba/chromap/index/** - - tests/modules/cnr-ibba/chromap/index/** - -circexplorer2/annotate: - - modules/cnr-ibba/circexplorer2/annotate/** - - tests/modules/cnr-ibba/circexplorer2/annotate/** - -circexplorer2/parse: - - modules/cnr-ibba/circexplorer2/parse/** - - tests/modules/cnr-ibba/circexplorer2/parse/** - -clonalframeml: - - modules/cnr-ibba/clonalframeml/** - - tests/modules/cnr-ibba/clonalframeml/** - -cmseq/polymut: - - modules/cnr-ibba/cmseq/polymut/** - - tests/modules/cnr-ibba/cmseq/polymut/** - -cnvkit/antitarget: - - modules/cnr-ibba/cnvkit/antitarget/** - - tests/modules/cnr-ibba/cnvkit/antitarget/** - -cnvkit/batch: - - modules/cnr-ibba/cnvkit/batch/** - - tests/modules/cnr-ibba/cnvkit/batch/** - -cnvkit/reference: - - modules/cnr-ibba/cnvkit/reference/** - - tests/modules/cnr-ibba/cnvkit/reference/** - -concoct/concoct: - - modules/cnr-ibba/concoct/concoct/** - - tests/modules/cnr-ibba/concoct/concoct/** - -concoct/concoctcoveragetable: - - modules/cnr-ibba/concoct/concoctcoveragetable/** - - tests/modules/cnr-ibba/concoct/concoctcoveragetable/** - -concoct/cutupfasta: - - modules/cnr-ibba/concoct/cutupfasta/** - - tests/modules/cnr-ibba/concoct/cutupfasta/** - -concoct/mergecutupclustering: - - modules/cnr-ibba/concoct/mergecutupclustering/** - - tests/modules/cnr-ibba/concoct/mergecutupclustering/** - -controlfreec/assesssignificance: - - modules/cnr-ibba/controlfreec/assesssignificance/** - - tests/modules/cnr-ibba/controlfreec/assesssignificance/** - -controlfreec/freec: - - modules/cnr-ibba/controlfreec/freec/** - - tests/modules/cnr-ibba/controlfreec/freec/** - -controlfreec/freec2bed: - - modules/cnr-ibba/controlfreec/freec2bed/** - - tests/modules/cnr-ibba/controlfreec/freec2bed/** - -controlfreec/freec2circos: - - modules/cnr-ibba/controlfreec/freec2circos/** - - tests/modules/cnr-ibba/controlfreec/freec2circos/** - -controlfreec/makegraph: - - modules/cnr-ibba/controlfreec/makegraph/** - - tests/modules/cnr-ibba/controlfreec/makegraph/** - -cooler/cload: - - modules/cnr-ibba/cooler/cload/** - - tests/modules/cnr-ibba/cooler/cload/** - -cooler/digest: - - modules/cnr-ibba/cooler/digest/** - - tests/modules/cnr-ibba/cooler/digest/** - -cooler/dump: - - modules/cnr-ibba/cooler/dump/** - - tests/modules/cnr-ibba/cooler/dump/** - -cooler/merge: - - modules/cnr-ibba/cooler/merge/** - - tests/modules/cnr-ibba/cooler/merge/** - -cooler/zoomify: - - modules/cnr-ibba/cooler/zoomify/** - - tests/software/cooler/zoomify/** - -crumble: - - modules/cnr-ibba/crumble/** - - tests/modules/cnr-ibba/crumble/** - -csvtk/concat: - - modules/cnr-ibba/csvtk/concat/** - - tests/modules/cnr-ibba/csvtk/concat/** - -csvtk/split: - - modules/cnr-ibba/csvtk/split/** - - tests/modules/cnr-ibba/csvtk/split/** - -custom/dumpsoftwareversions: - - modules/cnr-ibba/custom/dumpsoftwareversions/** - - tests/modules/cnr-ibba/custom/dumpsoftwareversions/** - -custom/getchromsizes: - - modules/cnr-ibba/custom/getchromsizes/** - - tests/modules/cnr-ibba/custom/getchromsizes/** - -custom/sratoolsncbisettings: - - modules/cnr-ibba/custom/sratoolsncbisettings/** - - tests/modules/cnr-ibba/custom/sratoolsncbisettings/** - -cutadapt: - - modules/cnr-ibba/cutadapt/** - - tests/modules/cnr-ibba/cutadapt/** - -damageprofiler: - - modules/cnr-ibba/damageprofiler/** - - tests/modules/cnr-ibba/damageprofiler/** - -dastool/dastool: - - modules/cnr-ibba/dastool/dastool/** - - tests/modules/cnr-ibba/dastool/dastool/** - -dastool/fastatocontig2bin: - - modules/cnr-ibba/dastool/fastatocontig2bin/** - - tests/modules/cnr-ibba/dastool/fastatocontig2bin/** - -dastool/scaffolds2bin: - - modules/cnr-ibba/dastool/scaffolds2bin/** - - tests/modules/cnr-ibba/dastool/scaffolds2bin/** - -dedup: - - modules/cnr-ibba/dedup/** - - tests/modules/cnr-ibba/dedup/** - -deeparg/downloaddata: - - modules/cnr-ibba/deeparg/downloaddata/** - - tests/modules/cnr-ibba/deeparg/downloaddata/** - -deeparg/predict: - - modules/cnr-ibba/deeparg/predict/** - - tests/modules/cnr-ibba/deeparg/predict/** - -deepbgc/download: - - modules/cnr-ibba/deepbgc/download/** - - tests/modules/cnr-ibba/deepbgc/download/** - -deepbgc/pipeline: - - modules/cnr-ibba/deepbgc/pipeline/** - - tests/modules/cnr-ibba/deepbgc/pipeline/** - -deeptools/bamcoverage: - - modules/cnr-ibba/deeptools/bamcoverage/** - - tests/modules/cnr-ibba/deeptools/bamcoverage/** - -deeptools/computematrix: - - modules/cnr-ibba/deeptools/computematrix/** - - tests/modules/cnr-ibba/deeptools/computematrix/** - -deeptools/plotfingerprint: - - modules/cnr-ibba/deeptools/plotfingerprint/** - - tests/modules/cnr-ibba/deeptools/plotfingerprint/** - -deeptools/plotheatmap: - - modules/cnr-ibba/deeptools/plotheatmap/** - - tests/modules/cnr-ibba/deeptools/plotheatmap/** - -deeptools/plotprofile: - - modules/cnr-ibba/deeptools/plotprofile/** - - tests/modules/cnr-ibba/deeptools/plotprofile/** - -deepvariant: - - modules/cnr-ibba/deepvariant/** - - tests/modules/cnr-ibba/deepvariant/** - -delly/call: - - modules/cnr-ibba/delly/call/** - - tests/modules/cnr-ibba/delly/call/** - -deseq2/differential: - - modules/cnr-ibba/deseq2/differential/** - - tests/modules/cnr-ibba/deseq2/differential/** - -diamond/blastp: - - modules/cnr-ibba/diamond/blastp/** - - tests/modules/cnr-ibba/diamond/blastp/** - -diamond/blastx: - - modules/cnr-ibba/diamond/blastx/** - - tests/modules/cnr-ibba/diamond/blastx/** - -diamond/makedb: - - modules/cnr-ibba/diamond/makedb/** - - tests/modules/cnr-ibba/diamond/makedb/** - -dragmap/align: - - modules/cnr-ibba/dragmap/align/** - - tests/modules/cnr-ibba/dragmap/align/** - -dragmap/hashtable: - - modules/cnr-ibba/dragmap/hashtable/** - - tests/modules/cnr-ibba/dragmap/hashtable/** - -dragonflye: - - modules/cnr-ibba/dragonflye/** - - tests/modules/cnr-ibba/dragonflye/** - -dshbio/exportsegments: - - modules/cnr-ibba/dshbio/exportsegments/** - - tests/modules/cnr-ibba/dshbio/exportsegments/** - -dshbio/filterbed: - - modules/cnr-ibba/dshbio/filterbed/** - - tests/modules/cnr-ibba/dshbio/filterbed/** - -dshbio/filtergff3: - - modules/cnr-ibba/dshbio/filtergff3/** - - tests/modules/cnr-ibba/dshbio/filtergff3/** - -dshbio/splitbed: - - modules/cnr-ibba/dshbio/splitbed/** - - tests/modules/cnr-ibba/dshbio/splitbed/** - -dshbio/splitgff3: - - modules/cnr-ibba/dshbio/splitgff3/** - - tests/modules/cnr-ibba/dshbio/splitgff3/** - -duphold: - - modules/cnr-ibba/duphold/** - - tests/modules/cnr-ibba/duphold/** - -ectyper: - - modules/cnr-ibba/ectyper/** - - tests/modules/cnr-ibba/ectyper/** - -eido/convert: - - modules/cnr-ibba/eido/convert/** - - tests/modules/cnr-ibba/eido/convert/** - -eido/validate: - - modules/cnr-ibba/eido/validate/** - - tests/modules/cnr-ibba/eido/validate/** - -elprep/filter: - - modules/cnr-ibba/elprep/filter/** - - tests/modules/cnr-ibba/elprep/filter/** - -elprep/merge: - - modules/cnr-ibba/elprep/merge/** - - tests/modules/cnr-ibba/elprep/merge/** - -elprep/split: - - modules/cnr-ibba/elprep/split/** - - tests/modules/cnr-ibba/elprep/split/** - -emboss/seqret: - - modules/cnr-ibba/emboss/seqret/** - - tests/modules/cnr-ibba/emboss/seqret/** - -emmtyper: - - modules/cnr-ibba/emmtyper/** - - tests/modules/cnr-ibba/emmtyper/** - -endorspy: - - modules/cnr-ibba/endorspy/** - - tests/modules/cnr-ibba/endorspy/** - -ensemblvep: - - modules/cnr-ibba/ensemblvep/** - - tests/modules/cnr-ibba/ensemblvep/** - -entrezdirect/esearch: - - modules/cnr-ibba/entrezdirect/esearch/** - - tests/modules/cnr-ibba/entrezdirect/esearch/** - -entrezdirect/esummary: - - modules/cnr-ibba/entrezdirect/esummary/** - - tests/modules/cnr-ibba/entrezdirect/esummary/** - -entrezdirect/xtract: - - modules/cnr-ibba/entrezdirect/xtract/** - - tests/modules/cnr-ibba/entrezdirect/xtract/** - -epang: - - modules/cnr-ibba/epang/** - - tests/modules/cnr-ibba/epang/ - -expansionhunter: - - modules/cnr-ibba/expansionhunter/** - - tests/modules/cnr-ibba/expansionhunter/** - -expansionhunterdenovo/merge: - - modules/cnr-ibba/expansionhunterdenovo/merge/** - - tests/modules/cnr-ibba/expansionhunterdenovo/merge/** - -expansionhunterdenovo/profile: - - modules/cnr-ibba/expansionhunterdenovo/profile/** - - tests/modules/cnr-ibba/expansionhunterdenovo/profile/** - -falco: - - modules/cnr-ibba/falco/** - - tests/modules/cnr-ibba/falco/** - -faqcs: - - modules/cnr-ibba/faqcs/** - - tests/modules/cnr-ibba/faqcs/** - -fargene: - - modules/cnr-ibba/fargene/** - - tests/modules/cnr-ibba/fargene/** - -fastani: - - modules/cnr-ibba/fastani/** - - tests/modules/cnr-ibba/fastani/** - -fastawindows: - - modules/cnr-ibba/fastawindows/** - - tests/modules/cnr-ibba/fastawindows/** - -fastk/fastk: - - modules/cnr-ibba/fastk/fastk/** - - tests/modules/cnr-ibba/fastk/fastk/** - -fastk/histex: - - modules/cnr-ibba/fastk/histex/** - - tests/modules/cnr-ibba/fastk/histex/** - -fastk/merge: - - modules/cnr-ibba/fastk/merge/** - - tests/modules/cnr-ibba/fastk/merge/** - -fastp: - - modules/cnr-ibba/fastp/** - - tests/modules/cnr-ibba/fastp/** - -fastqc: - - modules/cnr-ibba/fastqc/** - - tests/modules/cnr-ibba/fastqc/** - -fastqscan: - - modules/cnr-ibba/fastqscan/** - - tests/modules/cnr-ibba/fastqscan/** - -fasttree: - - modules/cnr-ibba/fasttree/** - - tests/modules/cnr-ibba/fasttree/** - -fcs/fcsadaptor: - - modules/cnr-ibba/fcs/fcsadaptor/** - - tests/modules/cnr-ibba/fcs/fcsadaptor/** - -ffq: - - modules/cnr-ibba/ffq/** - - tests/modules/cnr-ibba/ffq/** - -fgbio/callduplexconsensusreads: - - modules/cnr-ibba/fgbio/callduplexconsensusreads/** - - tests/modules/cnr-ibba/fgbio/callduplexconsensusreads/** - -fgbio/callmolecularconsensusreads: - - modules/cnr-ibba/fgbio/callmolecularconsensusreads/** - - tests/modules/cnr-ibba/fgbio/callmolecularconsensusreads/** - -fgbio/fastqtobam: - - modules/cnr-ibba/fgbio/fastqtobam/** - - tests/modules/cnr-ibba/fgbio/fastqtobam/** - -fgbio/filterconsensusreads: - - modules/cnr-ibba/fgbio/filterconsensusreads/** - - tests/modules/cnr-ibba/fgbio/filterconsensusreads/** - -fgbio/groupreadsbyumi: - - modules/cnr-ibba/fgbio/groupreadsbyumi/** - - tests/modules/cnr-ibba/fgbio/groupreadsbyumi/** - -fgbio/sortbam: - - modules/cnr-ibba/fgbio/sortbam/** - - tests/modules/cnr-ibba/fgbio/sortbam/** - -fgbio/zipperbams: - - modules/cnr-ibba/fgbio/zipperbams/** - - tests/modules/cnr-ibba/fgbio/zipperbams/** - -filtlong: - - modules/cnr-ibba/filtlong/** - - tests/modules/cnr-ibba/filtlong/** - -flash: - - modules/cnr-ibba/flash/** - - tests/modules/cnr-ibba/flash/** - -flye: - - modules/cnr-ibba/flye/** - - tests/modules/cnr-ibba/flye/** - -fq/lint: - - modules/cnr-ibba/fq/lint/** - - tests/modules/cnr-ibba/fq/lint/** + - modules/nf-core/bcftools/concat/** + - tests/modules/nf-core/bcftools/concat/** freebayes/chunk: - modules/cnr-ibba/freebayes/chunk/** @@ -955,1947 +26,26 @@ freebayes/splitbam: - modules/cnr-ibba/freebayes/splitbam/** - tests/modules/cnr-ibba/freebayes/splitbam/** -gamma/gamma: - - modules/cnr-ibba/gamma/gamma/** - - tests/modules/cnr-ibba/gamma/gamma/** - -gangstr: - - modules/cnr-ibba/gangstr/** - - tests/modules/cnr-ibba/gangstr/** - -gappa/examineassign: - - modules/cnr-ibba/gappa/examineassign/** - - tests/modules/cnr-ibba/gappa/examineassign/** - -gappa/examinegraft: - - modules/cnr-ibba/gappa/examinegraft/** - - tests/modules/cnr-ibba/gappa/examinegraft/** - -gappa/examineheattree: - - modules/cnr-ibba/gappa/examineheattree/** - - tests/modules/cnr-ibba/gappa/examineheattree/** - -gatk/indelrealigner: - - modules/cnr-ibba/gatk/indelrealigner/** - - tests/modules/cnr-ibba/gatk/indelrealigner/** - -gatk/realignertargetcreator: - - modules/cnr-ibba/gatk/realignertargetcreator/** - - tests/modules/cnr-ibba/gatk/realignertargetcreator/** - -gatk/unifiedgenotyper: - - modules/cnr-ibba/gatk/unifiedgenotyper/** - - tests/modules/cnr-ibba/gatk/unifiedgenotyper/** - -gatk4/applybqsr: - - modules/cnr-ibba/gatk4/applybqsr/** - - tests/modules/cnr-ibba/gatk4/applybqsr/** - -gatk4/applybqsrspark: - - modules/cnr-ibba/gatk4/applybqsrspark/** - - tests/modules/cnr-ibba/gatk4/applybqsrspark/** - -gatk4/applyvqsr: - - modules/cnr-ibba/gatk4/applyvqsr/** - - tests/modules/cnr-ibba/gatk4/applyvqsr/** - -gatk4/baserecalibrator: - - modules/cnr-ibba/gatk4/baserecalibrator/** - - tests/modules/cnr-ibba/gatk4/baserecalibrator/** - -gatk4/baserecalibratorspark: - - modules/cnr-ibba/gatk4/baserecalibratorspark/** - - tests/modules/cnr-ibba/gatk4/baserecalibratorspark/** - -gatk4/bedtointervallist: - - modules/cnr-ibba/gatk4/bedtointervallist/** - - tests/modules/cnr-ibba/gatk4/bedtointervallist/** - -gatk4/calculatecontamination: - - modules/cnr-ibba/gatk4/calculatecontamination/** - - tests/modules/cnr-ibba/gatk4/calculatecontamination/** - -gatk4/calibratedragstrmodel: - - modules/cnr-ibba/gatk4/calibratedragstrmodel/** - - tests/modules/cnr-ibba/gatk4/calibratedragstrmodel/** - -gatk4/cnnscorevariants: - - modules/cnr-ibba/gatk4/cnnscorevariants/** - - tests/modules/cnr-ibba/gatk4/cnnscorevariants/** - -gatk4/collectreadcounts: - - modules/cnr-ibba/gatk4/collectreadcounts/** - - tests/modules/cnr-ibba/gatk4/collectreadcounts/** - -gatk4/collectsvevidence: - - modules/cnr-ibba/gatk4/collectsvevidence/** - - tests/modules/cnr-ibba/gatk4/collectsvevidence/** - -gatk4/combinegvcfs: - - modules/cnr-ibba/gatk4/combinegvcfs/** - - tests/modules/cnr-ibba/gatk4/combinegvcfs/** - -gatk4/composestrtablefile: - - modules/cnr-ibba/gatk4/composestrtablefile/** - - tests/modules/cnr-ibba/gatk4/composestrtablefile/** - -gatk4/condensedepthevidence: - - modules/cnr-ibba/gatk4/condensedepthevidence/** - - tests/modules/cnr-ibba/gatk4/condensedepthevidence/** - -gatk4/createsequencedictionary: - - modules/cnr-ibba/gatk4/createsequencedictionary/** - - tests/modules/cnr-ibba/gatk4/createsequencedictionary/** - -gatk4/createsomaticpanelofnormals: - - modules/cnr-ibba/gatk4/createsomaticpanelofnormals/** - - tests/modules/cnr-ibba/gatk4/createsomaticpanelofnormals/** +samtools/coverage: + - modules/nf-core/samtools/coverage/** + - tests/modules/nf-core/samtools/coverage/** -gatk4/estimatelibrarycomplexity: - - modules/cnr-ibba/gatk4/estimatelibrarycomplexity/** - - tests/modules/cnr-ibba/gatk4/estimatelibrarycomplexity/** +samtools/flagstat: + - modules/nf-core/samtools/flagstat/** + - tests/modules/nf-core/samtools/flagstat/** -gatk4/fastqtosam: - - modules/cnr-ibba/gatk4/fastqtosam/** - - tests/modules/cnr-ibba/gatk4/fastqtosam/** +samtools/idxstats: + - modules/nf-core/samtools/idxstats/** + - tests/modules/nf-core/samtools/idxstats/** -gatk4/filtermutectcalls: - - modules/cnr-ibba/gatk4/filtermutectcalls/** - - tests/modules/cnr-ibba/gatk4/filtermutectcalls/** +samtools/stats: + - modules/nf-core/samtools/stats/** + - tests/modules/nf-core/samtools/stats/** -gatk4/filtervarianttranches: - - modules/cnr-ibba/gatk4/filtervarianttranches/** - - tests/modules/cnr-ibba/gatk4/filtervarianttranches/** - -gatk4/gatherbqsrreports: - - modules/cnr-ibba/gatk4/gatherbqsrreports/** - - tests/modules/cnr-ibba/gatk4/gatherbqsrreports/** - -gatk4/gatherpileupsummaries: - - modules/cnr-ibba/gatk4/gatherpileupsummaries/** - - tests/modules/cnr-ibba/gatk4/gatherpileupsummaries/** - -gatk4/genomicsdbimport: - - modules/cnr-ibba/gatk4/genomicsdbimport/** - - tests/modules/cnr-ibba/gatk4/genomicsdbimport/** - -gatk4/genotypegvcfs: - - modules/cnr-ibba/gatk4/genotypegvcfs/** - - tests/modules/cnr-ibba/gatk4/genotypegvcfs/** - -gatk4/getpileupsummaries: - - modules/cnr-ibba/gatk4/getpileupsummaries/** - - tests/modules/cnr-ibba/gatk4/getpileupsummaries/** - -gatk4/haplotypecaller: - - modules/cnr-ibba/gatk4/haplotypecaller/** - - tests/modules/cnr-ibba/gatk4/haplotypecaller/** - -gatk4/indexfeaturefile: - - modules/cnr-ibba/gatk4/indexfeaturefile/** - - tests/modules/cnr-ibba/gatk4/indexfeaturefile/** - -gatk4/intervallisttobed: - - modules/cnr-ibba/gatk4/intervallisttobed/** - - tests/modules/cnr-ibba/gatk4/intervallisttobed/** - -gatk4/intervallisttools: - - modules/cnr-ibba/gatk4/intervallisttools/** - - tests/modules/cnr-ibba/gatk4/intervallisttools/** - -gatk4/learnreadorientationmodel: - - modules/cnr-ibba/gatk4/learnreadorientationmodel/** - - tests/modules/cnr-ibba/gatk4/learnreadorientationmodel/** - -gatk4/leftalignandtrimvariants: - - modules/cnr-ibba/gatk4/leftalignandtrimvariants/** - - tests/modules/cnr-ibba/gatk4/leftalignandtrimvariants/** - -gatk4/markduplicates: - - modules/cnr-ibba/gatk4/markduplicates/** - - tests/modules/cnr-ibba/gatk4/markduplicates/** - -gatk4/markduplicatesspark: - - modules/cnr-ibba/gatk4/markduplicatesspark/** - - tests/modules/cnr-ibba/gatk4/markduplicatesspark/** - -gatk4/mergebamalignment: - - modules/cnr-ibba/gatk4/mergebamalignment/** - - tests/modules/cnr-ibba/gatk4/mergebamalignment/** - -gatk4/mergemutectstats: - - modules/cnr-ibba/gatk4/mergemutectstats/** - - tests/modules/cnr-ibba/gatk4/mergemutectstats/** - -gatk4/mergevcfs: - - modules/cnr-ibba/gatk4/mergevcfs/** - - tests/modules/cnr-ibba/gatk4/mergevcfs/** - -gatk4/mutect2: - - modules/cnr-ibba/gatk4/mutect2/** - - tests/modules/cnr-ibba/gatk4/mutect2/** - -gatk4/printsvevidence: - - modules/cnr-ibba/gatk4/printsvevidence/** - - tests/modules/cnr-ibba/gatk4/printsvevidence/** - -gatk4/reblockgvcf: - - modules/cnr-ibba/gatk4/reblockgvcf/** - - tests/modules/cnr-ibba/gatk4/reblockgvcf/** - -gatk4/revertsam: - - modules/cnr-ibba/gatk4/revertsam/** - - tests/modules/cnr-ibba/gatk4/revertsam/** - -gatk4/samtofastq: - - modules/cnr-ibba/gatk4/samtofastq/** - - tests/modules/cnr-ibba/gatk4/samtofastq/** - -gatk4/selectvariants: - - modules/cnr-ibba/gatk4/selectvariants/** - - tests/modules/cnr-ibba/gatk4/selectvariants/** - -gatk4/shiftfasta: - - modules/cnr-ibba/gatk4/shiftfasta/** - - tests/modules/cnr-ibba/gatk4/shiftfasta/** - -gatk4/sitedepthtobaf: - - modules/cnr-ibba/gatk4/sitedepthtobaf/** - - tests/modules/cnr-ibba/gatk4/sitedepthtobaf/** - -gatk4/splitintervals: - - modules/cnr-ibba/gatk4/splitintervals/** - - tests/modules/cnr-ibba/gatk4/splitintervals/** - -gatk4/splitncigarreads: - - modules/cnr-ibba/gatk4/splitncigarreads/** - - tests/modules/cnr-ibba/gatk4/splitncigarreads/** - -gatk4/svannotate: - - modules/cnr-ibba/gatk4/svannotate/** - - tests/modules/cnr-ibba/gatk4/svannotate/** - -gatk4/svcluster: - - modules/cnr-ibba/gatk4/svcluster/** - - tests/modules/cnr-ibba/gatk4/svcluster/** - -gatk4/variantfiltration: - - modules/cnr-ibba/gatk4/variantfiltration/** - - tests/modules/cnr-ibba/gatk4/variantfiltration/** - -gatk4/variantrecalibrator: - - modules/cnr-ibba/gatk4/variantrecalibrator/** - - tests/modules/cnr-ibba/gatk4/variantrecalibrator/** - -gecco/run: - - modules/cnr-ibba/gecco/run/** - - tests/modules/cnr-ibba/gecco/run/** - -genescopefk: - - modules/cnr-ibba/genescopefk/** - - tests/modules/cnr-ibba/genescopefk/** - -genmap/index: - - modules/cnr-ibba/genmap/index/** - - tests/modules/cnr-ibba/genmap/index/** - -genmap/mappability: - - modules/cnr-ibba/genmap/mappability/** - - tests/modules/cnr-ibba/genmap/mappability/** - -genmod/annotate: - - modules/cnr-ibba/genmod/annotate/** - - tests/modules/cnr-ibba/genmod/annotate/** - -genmod/compound: - - modules/cnr-ibba/genmod/compound/** - - tests/modules/cnr-ibba/genmod/compound/** - -genmod/models: - - modules/cnr-ibba/genmod/models/** - - tests/modules/cnr-ibba/genmod/models/** - -genmod/score: - - modules/cnr-ibba/genmod/score/** - - tests/modules/cnr-ibba/genmod/score/** - -genomescope2: - - modules/cnr-ibba/genomescope2/** - - tests/modules/cnr-ibba/genomescope2/** - -genotyphi/parse: - - modules/cnr-ibba/genotyphi/parse/** - - tests/modules/cnr-ibba/genotyphi/parse/** - -genrich: - - modules/cnr-ibba/genrich/** - - tests/modules/cnr-ibba/genrich/** - -gfaffix: - - modules/cnr-ibba/gfaffix/** - - tests/modules/cnr-ibba/gfaffix/** - -gffread: - - modules/cnr-ibba/gffread/** - - tests/modules/cnr-ibba/gffread/** - -glimpse/chunk: - - modules/cnr-ibba/glimpse/chunk/** - - tests/modules/cnr-ibba/glimpse/chunk/** - -glnexus: - - modules/cnr-ibba/glnexus/** - - tests/modules/cnr-ibba/glnexus/** - -goat/taxonsearch: - - modules/cnr-ibba/goat/taxonsearch/** - - tests/modules/cnr-ibba/goat/taxonsearch/** - -graphmap2/align: - - modules/cnr-ibba/graphmap2/align/** - - tests/modules/cnr-ibba/graphmap2/align/** - -graphmap2/index: - - modules/cnr-ibba/graphmap2/index/** - - tests/modules/cnr-ibba/graphmap2/index/** - -gstama/collapse: - - modules/cnr-ibba/gstama/collapse/** - - tests/modules/cnr-ibba/gstama/collapse/** - -gstama/merge: - - modules/cnr-ibba/gstama/merge/** - - tests/modules/cnr-ibba/gstama/merge/** - -gstama/polyacleanup: - - modules/cnr-ibba/gstama/polyacleanup/** - - tests/modules/cnr-ibba/gstama/polyacleanup/** - -gtdbtk/classifywf: - - modules/cnr-ibba/gtdbtk/classifywf/** - - tests/modules/cnr-ibba/gtdbtk/classifywf/** - -gubbins: - - modules/cnr-ibba/gubbins/** - - tests/modules/cnr-ibba/gubbins/** - -gunc/downloaddb: - - modules/cnr-ibba/gunc/downloaddb/** - - tests/modules/cnr-ibba/gunc/downloaddb/** - -gunc/run: - - modules/cnr-ibba/gunc/run/** - - tests/modules/cnr-ibba/gunc/run/** - -gunzip: - - modules/cnr-ibba/gunzip/** - - tests/modules/cnr-ibba/gunzip/** - -gvcftools/extractvariants: - - modules/cnr-ibba/gvcftools/extractvariants/** - - tests/modules/cnr-ibba/gvcftools/extractvariants/** - -hamronization/abricate: - - modules/cnr-ibba/hamronization/abricate/** - - tests/modules/cnr-ibba/hamronization/abricate/** - -hamronization/amrfinderplus: - - modules/cnr-ibba/hamronization/amrfinderplus/** - - tests/modules/cnr-ibba/hamronization/amrfinderplus/** - -hamronization/deeparg: - - modules/cnr-ibba/hamronization/deeparg/** - - tests/modules/cnr-ibba/hamronization/deeparg/** - -hamronization/fargene: - - modules/cnr-ibba/hamronization/fargene/** - - tests/modules/cnr-ibba/hamronization/fargene/** - -hamronization/rgi: - - modules/cnr-ibba/hamronization/rgi/** - - tests/modules/cnr-ibba/hamronization/rgi/** - -hamronization/summarize: - - modules/cnr-ibba/hamronization/summarize/** - - tests/modules/cnr-ibba/hamronization/summarize/** - -hapibd: - - modules/cnr-ibba/hapibd/** - - tests/modules/cnr-ibba/hapibd/** - -haplocheck: - - modules/cnr-ibba/haplocheck/** - - tests/modules/cnr-ibba/haplocheck/** - -haplogrep2/classify: - - modules/cnr-ibba/haplogrep2/classify/** - - tests/modules/cnr-ibba/haplogrep2/classify/** - -happy/happy: - - modules/cnr-ibba/happy/happy/** - - tests/modules/cnr-ibba/happy/happy/** - -happy/prepy: - - modules/cnr-ibba/happy/prepy/** - - tests/modules/cnr-ibba/happy/prepy/** - -hicap: - - modules/cnr-ibba/hicap/** - - tests/modules/cnr-ibba/hicap/** - -hifiasm: - - modules/cnr-ibba/hifiasm/** - - tests/modules/cnr-ibba/hifiasm/** - -hisat2/align: - - modules/cnr-ibba/hisat2/align/** - - modules/cnr-ibba/hisat2/build/** - - modules/cnr-ibba/hisat2/extractsplicesites/** - - tests/modules/cnr-ibba/hisat2/align/** - -hisat2/build: - - modules/cnr-ibba/hisat2/build/** - - modules/cnr-ibba/hisat2/extractsplicesites/** - - tests/modules/cnr-ibba/hisat2/build_test/** - -hisat2/extractsplicesites: - - modules/cnr-ibba/hisat2/extractsplicesites/** - - tests/modules/cnr-ibba/hisat2/extractsplicesites/** - -hmmcopy/gccounter: - - modules/cnr-ibba/hmmcopy/gccounter/** - - tests/modules/cnr-ibba/hmmcopy/gccounter/** - -hmmcopy/generatemap: - - modules/cnr-ibba/hmmcopy/generatemap/** - - tests/modules/cnr-ibba/hmmcopy/generatemap/** - -hmmcopy/mapcounter: - - modules/cnr-ibba/hmmcopy/mapcounter/** - - tests/modules/cnr-ibba/hmmcopy/mapcounter/** - -hmmcopy/readcounter: - - modules/cnr-ibba/hmmcopy/readcounter/** - - tests/modules/cnr-ibba/hmmcopy/readcounter/** - -hmmer/eslalimask: - - modules/cnr-ibba/hmmer/eslalimask/** - - tests/modules/cnr-ibba/hmmer/eslalimask/** - -hmmer/eslreformat: - - modules/cnr-ibba/hmmer/eslreformat/** - - tests/modules/cnr-ibba/hmmer/eslreformat/** - -hmmer/hmmalign: - - modules/cnr-ibba/hmmer/hmmalign/** - - tests/modules/cnr-ibba/hmmer/hmmalign/** - -hmmer/hmmbuild: - - modules/cnr-ibba/hmmer/hmmbuild/** - - tests/modules/cnr-ibba/hmmer/hmmbuild/** - -hmmer/hmmsearch: - - modules/cnr-ibba/hmmer/hmmsearch/** - - tests/modules/cnr-ibba/hmmer/hmmsearch/** - -hmtnote: - - modules/cnr-ibba/hmtnote/** - - tests/modules/cnr-ibba/hmtnote/** - -homer/annotatepeaks: - - modules/cnr-ibba/homer/annotatepeaks/** - - tests/modules/cnr-ibba/homer/annotatepeaks/** - -homer/findpeaks: - - modules/cnr-ibba/homer/findpeaks/** - - modules/cnr-ibba/homer/maketagdirectory/** - - tests/modules/cnr-ibba/homer/findpeaks/** - -homer/maketagdirectory: - - modules/cnr-ibba/homer/maketagdirectory/** - - tests/modules/cnr-ibba/homer/maketagdirectory/** - -homer/makeucscfile: - - modules/cnr-ibba/homer/makeucscfile/** - - tests/modules/cnr-ibba/homer/makeucscfile/** - -homer/pos2bed: - - modules/cnr-ibba/homer/pos2bed/** - - modules/cnr-ibba/homer/maketagdirectory/** - - modules/cnr-ibba/homer/findpeaks/** - - tests/modules/cnr-ibba/homer/pos2bed/** - -hpsuissero: - - modules/cnr-ibba/hpsuissero/** - - tests/modules/cnr-ibba/hpsuissero/** - -ichorcna/createpon: - - modules/cnr-ibba/ichorcna/createpon/** - - tests/modules/cnr-ibba/ichorcna/createpon/** - -ichorcna/run: - - modules/cnr-ibba/ichorcna/run/** - - tests/modules/cnr-ibba/ichorcna/run/** - -idr: - - modules/cnr-ibba/idr/** - - tests/modules/cnr-ibba/idr/** - -imputeme/vcftoprs: - - modules/cnr-ibba/imputeme/vcftoprs/** - - tests/modules/cnr-ibba/imputeme/vcftoprs/** - -instrain/profile: - - modules/cnr-ibba/instrain/profile/** - - tests/modules/cnr-ibba/instrain/profile/** - -iqtree: - - modules/cnr-ibba/iqtree/** - - tests/modules/cnr-ibba/iqtree/** - -ismapper: - - modules/cnr-ibba/ismapper/** - - tests/modules/cnr-ibba/ismapper/** - -isoseq3/cluster: - - modules/cnr-ibba/isoseq3/cluster/** - - tests/modules/cnr-ibba/isoseq3/cluster/** - -isoseq3/refine: - - modules/cnr-ibba/isoseq3/refine/** - - tests/modules/cnr-ibba/isoseq3/refine/** - -ivar/consensus: - - modules/cnr-ibba/ivar/consensus/** - - tests/modules/cnr-ibba/ivar/consensus/** - -ivar/trim: - - modules/cnr-ibba/ivar/trim/** - - tests/modules/cnr-ibba/ivar/trim/** - -ivar/variants: - - modules/cnr-ibba/ivar/variants/** - - tests/modules/cnr-ibba/ivar/variants/** - -jupyternotebook: - - modules/cnr-ibba/jupyternotebook/** - - tests/modules/cnr-ibba/jupyternotebook/** - -kaiju/kaiju: - - modules/cnr-ibba/kaiju/kaiju/** - - tests/modules/cnr-ibba/kaiju/kaiju/** - -kaiju/kaiju2krona: - - modules/cnr-ibba/kaiju/kaiju2krona/** - - tests/modules/cnr-ibba/kaiju/kaiju2krona/** - -kaiju/kaiju2table: - - modules/cnr-ibba/kaiju/kaiju2table/** - - tests/modules/cnr-ibba/kaiju/kaiju2table/** - -kallisto/index: - - modules/cnr-ibba/kallisto/index/** - - tests/modules/cnr-ibba/kallisto/index/** - -kallistobustools/count: - - modules/cnr-ibba/kallistobustools/count/** - - tests/modules/cnr-ibba/kallistobustools/count/** - -kallistobustools/ref: - - modules/cnr-ibba/kallistobustools/ref/** - - tests/modules/cnr-ibba/kallistobustools/ref/** - -kat/hist: - - modules/cnr-ibba/kat/hist/** - - tests/modules/cnr-ibba/kat/hist/** - -khmer/normalizebymedian: - - modules/cnr-ibba/khmer/normalizebymedian/** - - tests/modules/cnr-ibba/khmer/normalizebymedian/** - -khmer/uniquekmers: - - modules/cnr-ibba/khmer/uniquekmers/** - - tests/modules/cnr-ibba/khmer/uniquekmers/** - -kleborate: - - modules/cnr-ibba/kleborate/** - - tests/modules/cnr-ibba/kleborate/** - -kofamscan: - - modules/cnr-ibba/kofamscan/** - - tests/modules/cnr-ibba/kofamscan/** - -kraken2/kraken2: - - modules/cnr-ibba/kraken2/kraken2/** - - modules/cnr-ibba/untar/** - - tests/modules/cnr-ibba/kraken2/kraken2/** - -krakentools/combinekreports: - - modules/cnr-ibba/krakentools/combinekreports/** - - tests/modules/cnr-ibba/krakentools/combinekreports/** - -krakentools/kreport2krona: - - modules/cnr-ibba/krakentools/kreport2krona/** - - tests/modules/cnr-ibba/krakentools/kreport2krona/** - -krakenuniq/build: - - modules/cnr-ibba/krakenuniq/build/** - - tests/modules/cnr-ibba/krakenuniq/build/** - -krakenuniq/download: - - modules/cnr-ibba/krakenuniq/download/** - - tests/modules/cnr-ibba/krakenuniq/download/** - -krakenuniq/preloadedkrakenuniq: - - modules/cnr-ibba/krakenuniq/preloadedkrakenuniq/** - - tests/modules/cnr-ibba/krakenuniq/preloadedkrakenuniq/** - -krona/kronadb: - - modules/cnr-ibba/krona/kronadb/** - - tests/modules/cnr-ibba/krona/kronadb/** - -krona/ktimporttaxonomy: - - modules/cnr-ibba/krona/ktimporttaxonomy/** - - tests/modules/cnr-ibba/krona/ktimporttaxonomy/** - -krona/ktimporttext: - - modules/cnr-ibba/krona/ktimporttext/** - - tests/modules/cnr-ibba/krona/ktimporttext/** - -krona/ktupdatetaxonomy: - - modules/cnr-ibba/krona/ktupdatetaxonomy/** - - tests/modules/cnr-ibba/krona/ktupdatetaxonomy/** - -last/dotplot: - - modules/cnr-ibba/last/dotplot/** - - tests/modules/cnr-ibba/last/dotplot/** - -last/lastal: - - modules/cnr-ibba/last/lastal/** - - tests/modules/cnr-ibba/last/lastal/** - -last/lastdb: - - modules/cnr-ibba/last/lastdb/** - - tests/modules/cnr-ibba/last/lastdb/** - -last/mafconvert: - - modules/cnr-ibba/last/mafconvert/** - - tests/modules/cnr-ibba/last/mafconvert/** - -last/mafswap: - - modules/cnr-ibba/last/mafswap/** - - tests/modules/cnr-ibba/last/mafswap/** - -last/postmask: - - modules/cnr-ibba/last/postmask/** - - tests/modules/cnr-ibba/last/postmask/** - -last/split: - - modules/cnr-ibba/last/split/** - - tests/modules/cnr-ibba/last/split/** - -last/train: - - modules/cnr-ibba/last/train/** - - tests/modules/cnr-ibba/last/train/** - -leehom: - - modules/cnr-ibba/leehom/** - - tests/modules/cnr-ibba/leehom/** - -legsta: - - modules/cnr-ibba/legsta/** - - tests/modules/cnr-ibba/legsta/** - -lima: - - modules/cnr-ibba/lima/** - - tests/modules/cnr-ibba/lima/** - -lissero: - - modules/cnr-ibba/lissero/** - - tests/modules/cnr-ibba/lissero/** - -lofreq/call: - - modules/cnr-ibba/lofreq/call/** - - tests/modules/cnr-ibba/lofreq/call/** - -lofreq/callparallel: - - modules/cnr-ibba/lofreq/callparallel/** - - tests/modules/cnr-ibba/lofreq/callparallel/** - -lofreq/filter: - - modules/cnr-ibba/lofreq/filter/** - - tests/modules/cnr-ibba/lofreq/filter/** - -lofreq/indelqual: - - modules/cnr-ibba/lofreq/indelqual/** - - tests/modules/cnr-ibba/lofreq/indelqual/** - -macrel/contigs: - - modules/cnr-ibba/macrel/contigs/** - - tests/modules/cnr-ibba/macrel/contigs/** - -macs2/callpeak: - - modules/cnr-ibba/macs2/callpeak/** - - tests/modules/cnr-ibba/macs2/callpeak/** - -mafft: - - modules/cnr-ibba/mafft/** - - tests/modules/cnr-ibba/mafft/** - -mageck/count: - - modules/cnr-ibba/mageck/count/** - - tests/modules/cnr-ibba/mageck/count/** - -mageck/mle: - - modules/cnr-ibba/mageck/mle/** - - tests/modules/cnr-ibba/mageck/mle/** - -malt/build: - - modules/cnr-ibba/malt/build/** - - tests/modules/cnr-ibba/malt/build_test/** - -malt/run: - - modules/cnr-ibba/malt/run/** - - tests/modules/cnr-ibba/malt/run/** - -maltextract: - - modules/cnr-ibba/maltextract/** - - tests/modules/cnr-ibba/maltextract/** - -manta/convertinversion: - - modules/cnr-ibba/manta/convertinversion/** - - tests/modules/cnr-ibba/manta/convertinversion/** - -manta/germline: - - modules/cnr-ibba/manta/germline/** - - tests/modules/cnr-ibba/manta/germline/** - -manta/somatic: - - modules/cnr-ibba/manta/somatic/** - - tests/modules/cnr-ibba/manta/somatic/** - -manta/tumoronly: - - modules/cnr-ibba/manta/tumoronly/** - - tests/modules/cnr-ibba/manta/tumoronly/** - -mapdamage2: - - modules/cnr-ibba/mapdamage2/** - - tests/modules/cnr-ibba/mapdamage2/** - -mash/dist: - - modules/cnr-ibba/mash/dist/** - - tests/modules/cnr-ibba/mash/dist/** - -mash/screen: - - modules/cnr-ibba/mash/screen/** - - tests/modules/cnr-ibba/mash/screen/** - -mash/sketch: - - modules/cnr-ibba/mash/sketch/** - - tests/modules/cnr-ibba/mash/sketch/** - -mashtree: - - modules/cnr-ibba/mashtree/** - - tests/modules/cnr-ibba/mashtree/** - -maxbin2: - - modules/cnr-ibba/maxbin2/** - - tests/modules/cnr-ibba/maxbin2/** - -maxquant/lfq: - - modules/cnr-ibba/maxquant/lfq/** - - tests/modules/cnr-ibba/maxquant/lfq/** - -mcroni: - - modules/cnr-ibba/mcroni/** - - tests/modules/cnr-ibba/mcroni/** - -md5sum: - - modules/cnr-ibba/md5sum/** - - tests/modules/cnr-ibba/md5sum/** - -medaka: - - modules/cnr-ibba/medaka/** - - tests/modules/cnr-ibba/medaka/** - -megahit: - - modules/cnr-ibba/megahit/** - - tests/modules/cnr-ibba/megahit/** - -megan/daa2info: - - modules/cnr-ibba/megan/daa2info/** - - tests/modules/cnr-ibba/megan/daa2info/** - -megan/rma2info: - - modules/cnr-ibba/megan/rma2info/** - - tests/modules/cnr-ibba/megan/rma2info/** - -meningotype: - - modules/cnr-ibba/meningotype/** - - tests/modules/cnr-ibba/meningotype/** - -merqury: - - modules/cnr-ibba/merqury/** - - tests/modules/cnr-ibba/merqury/** - -merquryfk/katcomp: - - modules/cnr-ibba/merquryfk/katcomp/** - - tests/modules/cnr-ibba/merquryfk/katcomp/** - -merquryfk/katgc: - - modules/cnr-ibba/merquryfk/katgc/** - - tests/modules/cnr-ibba/merquryfk/katgc/** - -merquryfk/merquryfk: - - modules/cnr-ibba/merquryfk/merquryfk/** - - tests/modules/cnr-ibba/merquryfk/merquryfk/** - -merquryfk/ploidyplot: - - modules/cnr-ibba/merquryfk/ploidyplot/** - - tests/modules/cnr-ibba/merquryfk/ploidyplot/** - -meryl/count: - - modules/cnr-ibba/meryl/count/** - - tests/modules/cnr-ibba/meryl/count/** - -meryl/histogram: - - modules/cnr-ibba/meryl/histogram/** - - tests/modules/cnr-ibba/meryl/histogram/** - -meryl/unionsum: - - modules/cnr-ibba/meryl/unionsum/** - - tests/modules/cnr-ibba/meryl/unionsum/** - -metabat2/jgisummarizebamcontigdepths: - - modules/cnr-ibba/metabat2/jgisummarizebamcontigdepths/** - - tests/modules/cnr-ibba/metabat2/jgisummarizebamcontigdepths/** - -metabat2/metabat2: - - modules/cnr-ibba/metabat2/metabat2/** - - tests/modules/cnr-ibba/metabat2/metabat2/** - -metaphlan3/mergemetaphlantables: - - modules/cnr-ibba/metaphlan3/mergemetaphlantables/** - - tests/modules/cnr-ibba/metaphlan3/mergemetaphlantables/** - -metaphlan3/metaphlan3: - - modules/cnr-ibba/metaphlan3/metaphlan3/** - - tests/modules/cnr-ibba/metaphlan3/metaphlan3/** - -methyldackel/extract: - - modules/cnr-ibba/methyldackel/extract/** - - tests/modules/cnr-ibba/methyldackel/extract/** - -methyldackel/mbias: - - modules/cnr-ibba/methyldackel/mbias/** - - tests/modules/cnr-ibba/methyldackel/mbias/** - -minia: - - modules/cnr-ibba/minia/** - - tests/modules/cnr-ibba/minia/** - -miniasm: - - modules/cnr-ibba/miniasm/** - - tests/modules/cnr-ibba/miniasm/** - -minimap2/align: - - modules/cnr-ibba/minimap2/align/** - - tests/modules/cnr-ibba/minimap2/align/** - -minimap2/index: - - modules/cnr-ibba/minimap2/index/** - - tests/modules/cnr-ibba/minimap2/index/** - -miranda: - - modules/cnr-ibba/miranda/** - - tests/modules/cnr-ibba/miranda/** - -mlst: - - modules/cnr-ibba/mlst/** - - tests/modules/cnr-ibba/mlst/** - -mobsuite/recon: - - modules/cnr-ibba/mobsuite/recon/** - - tests/modules/cnr-ibba/mobsuite/recon/** - -mosdepth: - - modules/cnr-ibba/mosdepth/** - - tests/modules/cnr-ibba/mosdepth/** - -motus/downloaddb: - - modules/cnr-ibba/motus/downloaddb/** - - tests/modules/cnr-ibba/motus/downloaddb/** - -motus/merge: - - modules/cnr-ibba/motus/merge/** - - tests/modules/cnr-ibba/motus/merge/** - -motus/profile: - - modules/cnr-ibba/motus/profile/** - - tests/modules/cnr-ibba/motus/profile/** - -msisensor/msi: - - modules/cnr-ibba/msisensor/msi/** - - tests/modules/cnr-ibba/msisensor/msi/** - -msisensor/scan: - - modules/cnr-ibba/msisensor/scan/** - - tests/modules/cnr-ibba/msisensor/scan/** - -msisensor2/msi: - - modules/cnr-ibba/msisensor2/msi/** - - tests/modules/cnr-ibba/msisensor2/msi/** - -msisensor2/scan: - - modules/cnr-ibba/msisensor2/scan/** - - tests/modules/cnr-ibba/msisensor2/scan/** - -msisensorpro/msi_somatic: - - modules/cnr-ibba/msisensorpro/msi_somatic/** - - tests/modules/cnr-ibba/msisensorpro/msi_somatic/** - -msisensorpro/scan: - - modules/cnr-ibba/msisensorpro/scan/** - - tests/modules/cnr-ibba/msisensorpro/scan/** - -mtnucratio: - - modules/cnr-ibba/mtnucratio/** - - tests/modules/cnr-ibba/mtnucratio/** - -multiqc: - - modules/cnr-ibba/fastqc/** - - modules/cnr-ibba/multiqc/** - - tests/modules/cnr-ibba/multiqc/** - -multivcfanalyzer: - - modules/cnr-ibba/multivcfanalyzer/** - - tests/modules/cnr-ibba/multivcfanalyzer/** - -mummer: - - modules/cnr-ibba/mummer/** - - tests/modules/cnr-ibba/mummer/** - -muscle: - - modules/cnr-ibba/muscle/** - - tests/modules/cnr-ibba/muscle/** - -mykrobe/predict: - - modules/cnr-ibba/mykrobe/predict/** - - tests/modules/cnr-ibba/mykrobe/predict/** - -nanolyse: - - modules/cnr-ibba/nanolyse/** - - tests/modules/cnr-ibba/nanolyse/** - -nanomonsv/parse: - - modules/cnr-ibba/nanomonsv/parse/** - - tests/modules/cnr-ibba/nanomonsv/parse/** - -nanoplot: - - modules/cnr-ibba/nanoplot/** - - tests/modules/cnr-ibba/nanoplot/** - -ncbigenomedownload: - - modules/cnr-ibba/ncbigenomedownload/** - - tests/modules/cnr-ibba/ncbigenomedownload/** - -nextclade/datasetget: - - modules/cnr-ibba/nextclade/datasetget/** - - tests/modules/cnr-ibba/nextclade/datasetget/** - -nextclade/run: - - modules/cnr-ibba/nextclade/run/** - - tests/modules/cnr-ibba/nextclade/run/** - -nextgenmap: - - modules/cnr-ibba/nextgenmap/** - - tests/modules/cnr-ibba/nextgenmap/** - -ngmaster: - - modules/cnr-ibba/ngmaster/** - - tests/modules/cnr-ibba/ngmaster/** - -ngscheckmate/ncm: - - modules/cnr-ibba/ngscheckmate/ncm/** - - tests/modules/cnr-ibba/ngscheckmate/ncm/** - -nucmer: - - modules/cnr-ibba/nucmer/** - - tests/modules/cnr-ibba/nucmer/** - -odgi/build: - - modules/cnr-ibba/odgi/build/** - - tests/modules/cnr-ibba/odgi/build_test/** - -odgi/draw: - - modules/cnr-ibba/odgi/draw/** - - tests/modules/cnr-ibba/odgi/draw/** - -odgi/layout: - - modules/cnr-ibba/odgi/layout/** - - tests/modules/cnr-ibba/odgi/layout/** - -odgi/sort: - - modules/cnr-ibba/odgi/sort/** - - tests/modules/cnr-ibba/odgi/sort/** - -odgi/stats: - - modules/cnr-ibba/odgi/stats/** - - tests/modules/cnr-ibba/odgi/stats/** - -odgi/unchop: - - modules/cnr-ibba/odgi/unchop/** - - tests/modules/cnr-ibba/odgi/unchop/** - -odgi/view: - - modules/cnr-ibba/odgi/view/** - - tests/modules/cnr-ibba/odgi/view/** - -odgi/viz: - - modules/cnr-ibba/odgi/viz/** - - tests/modules/cnr-ibba/odgi/viz/** - -optitype: - - modules/cnr-ibba/optitype/** - - tests/modules/cnr-ibba/optitype/** - -pairix: - - modules/cnr-ibba/pairix/** - - tests/modules/cnr-ibba/pairix/** - -pairtools/dedup: - - modules/cnr-ibba/pairtools/dedup/** - - tests/modules/cnr-ibba/pairtools/dedup/** - -pairtools/flip: - - modules/cnr-ibba/pairtools/flip/** - - tests/modules/cnr-ibba/pairtools/flip/** - -pairtools/parse: - - modules/cnr-ibba/pairtools/parse/** - - tests/modules/cnr-ibba/pairtools/parse/** - -pairtools/restrict: - - modules/cnr-ibba/pairtools/restrict/** - - tests/modules/cnr-ibba/pairtools/restrict/** - -pairtools/select: - - modules/cnr-ibba/pairtools/select/** - - tests/modules/cnr-ibba/pairtools/select/** - -pairtools/sort: - - modules/cnr-ibba/pairtools/sort/** - - tests/modules/cnr-ibba/pairtools/sort/** - -panaroo/run: - - modules/cnr-ibba/panaroo/run/** - - tests/modules/cnr-ibba/panaroo/run/** - -pangolin: - - modules/cnr-ibba/pangolin/** - - tests/modules/cnr-ibba/pangolin/** - -paraclu: - - modules/cnr-ibba/paraclu/** - - tests/modules/cnr-ibba/paraclu/** - -pasty: - - modules/cnr-ibba/pasty/** - - tests/modules/cnr-ibba/pasty/** - -pbbam/pbmerge: - - modules/cnr-ibba/pbbam/pbmerge/** - - tests/modules/cnr-ibba/pbbam/pbmerge/** - -pbccs: - - modules/cnr-ibba/pbccs/** - - tests/modules/cnr-ibba/pbccs/** - -pbptyper: - - modules/cnr-ibba/pbptyper/** - - tests/modules/cnr-ibba/pbptyper/** - -pear: - - modules/cnr-ibba/pear/** - - tests/modules/cnr-ibba/pear/** - -peddy: - - modules/cnr-ibba/peddy/** - - tests/modules/cnr-ibba/peddy/** - -phantompeakqualtools: - - modules/cnr-ibba/phantompeakqualtools/** - - tests/modules/cnr-ibba/phantompeakqualtools/** - -phyloflash: - - modules/cnr-ibba/phyloflash/** - - tests/modules/cnr-ibba/phyloflash/** - -picard/addorreplacereadgroups: - - modules/cnr-ibba/picard/addorreplacereadgroups/** - - tests/modules/cnr-ibba/picard/addorreplacereadgroups/** - -picard/cleansam: - - modules/cnr-ibba/picard/cleansam/** - - tests/modules/cnr-ibba/picard/cleansam/** - -picard/collecthsmetrics: - - modules/cnr-ibba/picard/collecthsmetrics/** - - tests/modules/cnr-ibba/picard/collecthsmetrics/** - -picard/collectmultiplemetrics: - - modules/cnr-ibba/picard/collectmultiplemetrics/** - - tests/modules/cnr-ibba/picard/collectmultiplemetrics/** - -picard/collectwgsmetrics: - - modules/cnr-ibba/picard/collectwgsmetrics/** - - tests/modules/cnr-ibba/picard/collectwgsmetrics/** - -picard/createsequencedictionary: - - modules/cnr-ibba/picard/createsequencedictionary/** - - tests/modules/cnr-ibba/picard/createsequencedictionary/** - -picard/crosscheckfingerprints: - - modules/cnr-ibba/picard/crosscheckfingerprints/** - - tests/modules/cnr-ibba/picard/crosscheckfingerprints/** - -picard/fastqtosam: - - modules/cnr-ibba/picard/fastqtosam/** - - tests/modules/cnr-ibba/picard/fastqtosam/** - -picard/filtersamreads: - - modules/cnr-ibba/picard/filtersamreads/** - - tests/modules/cnr-ibba/picard/filtersamreads/** - -picard/fixmateinformation: - - modules/cnr-ibba/picard/fixmateinformation/** - - tests/modules/cnr-ibba/picard/fixmateinformation/** - -picard/liftovervcf: - - modules/cnr-ibba/picard/liftovervcf/** - - tests/modules/cnr-ibba/picard/liftovervcf/** - -picard/markduplicates: - - modules/cnr-ibba/picard/markduplicates/** - - tests/modules/cnr-ibba/picard/markduplicates/** - -picard/mergesamfiles: - - modules/cnr-ibba/picard/mergesamfiles/** - - tests/modules/cnr-ibba/picard/mergesamfiles/** - -picard/renamesampleinvcf: - - modules/cnr-ibba/picard/renamesampleinvcf/** - - tests/modules/cnr-ibba/picard/renamesampleinvcf/** - -picard/sortsam: - - modules/cnr-ibba/picard/sortsam/** - - tests/modules/cnr-ibba/picard/sortsam/** - -picard/sortvcf: - - modules/cnr-ibba/picard/sortvcf/** - - tests/modules/cnr-ibba/picard/sortvcf/** - -pints/caller: - - modules/cnr-ibba/pints/caller/** - - tests/modules/cnr-ibba/pints/caller/** - -pirate: - - modules/cnr-ibba/pirate/** - - tests/modules/cnr-ibba/pirate/** - -plasmidfinder: - - modules/cnr-ibba/plasmidfinder/** - - tests/modules/cnr-ibba/plasmidfinder/** - -plasmidid: - - modules/cnr-ibba/plasmidid/** - - tests/modules/cnr-ibba/plasmidid/** - -plink/extract: - - modules/cnr-ibba/plink/extract/** - - tests/modules/cnr-ibba/plink/extract/** - -plink/vcf: - - modules/cnr-ibba/plink/vcf/** - - tests/modules/cnr-ibba/plink/vcf/** - -plink2/extract: - - modules/cnr-ibba/plink2/extract/** - - tests/modules/cnr-ibba/plink2/extract/** - -plink2/score: - - modules/cnr-ibba/plink2/score/** - - tests/modules/cnr-ibba/plink2/score/** - -plink2/vcf: - - modules/cnr-ibba/plink2/vcf/** - - tests/modules/cnr-ibba/plink2/vcf/** - -pmdtools/filter: - - modules/cnr-ibba/pmdtools/filter/** - - tests/modules/cnr-ibba/pmdtools/filter/** - -porechop: - - modules/cnr-ibba/porechop/** - - tests/modules/cnr-ibba/porechop/** - -preseq/ccurve: - - modules/cnr-ibba/preseq/ccurve/** - - tests/modules/cnr-ibba/preseq/ccurve/** - -preseq/lcextrap: - - modules/cnr-ibba/preseq/lcextrap/** - - tests/modules/cnr-ibba/preseq/lcextrap/** - -pretextmap: - - modules/cnr-ibba/pretextmap/** - - tests/modules/cnr-ibba/pretextmap/** - -prinseqplusplus: - - modules/cnr-ibba/prinseqplusplus/** - - tests/modules/cnr-ibba/prinseqplusplus/** - -prodigal: - - modules/cnr-ibba/prodigal/** - - tests/modules/cnr-ibba/prodigal/** - -prokka: - - modules/cnr-ibba/prokka/** - - tests/modules/cnr-ibba/prokka/** - -pycoqc: - - modules/cnr-ibba/pycoqc/** - - tests/modules/cnr-ibba/pycoqc/** - -pydamage/analyze: - - modules/cnr-ibba/pydamage/analyze/** - - tests/modules/cnr-ibba/pydamage/analyze/** - -pydamage/filter: - - modules/cnr-ibba/pydamage/filter/** - - tests/modules/cnr-ibba/pydamage/filter/** - -qcat: - - modules/cnr-ibba/qcat/** - - tests/modules/cnr-ibba/qcat/** - -qualimap/bamqc: - - modules/cnr-ibba/qualimap/bamqc/** - - tests/modules/cnr-ibba/qualimap/bamqc/** - -qualimap/bamqccram: - - modules/cnr-ibba/qualimap/bamqccram/** - - tests/modules/cnr-ibba/qualimap/bamqccram/** - -quast: - - modules/cnr-ibba/quast/** - - tests/modules/cnr-ibba/quast/** - -racon: - - modules/cnr-ibba/racon/** - - tests/modules/cnr-ibba/racon/** - -rapidnj: - - modules/cnr-ibba/rapidnj/** - - tests/modules/cnr-ibba/rapidnj/** - -rasusa: - - modules/cnr-ibba/rasusa/** - - tests/modules/cnr-ibba/rasusa/** - -raven: - - modules/cnr-ibba/raven/** - - tests/modules/cnr-ibba/raven/** - -raxmlng: - - modules/cnr-ibba/raxmlng/** - - tests/modules/cnr-ibba/raxmlng/** - -rgi/main: - - modules/cnr-ibba/rgi/main/** - - tests/modules/cnr-ibba/rgi/main/** - -rhocall/annotate: - - modules/cnr-ibba/rhocall/annotate/** - - tests/modules/cnr-ibba/rhocall/annotate/** - -rmarkdownnotebook: - - modules/cnr-ibba/rmarkdownnotebook/** - - tests/modules/cnr-ibba/rmarkdownnotebook/** - -roary: - - modules/cnr-ibba/roary/** - - tests/modules/cnr-ibba/roary/** - -rsem/calculateexpression: - - modules/cnr-ibba/rsem/calculateexpression/** - - tests/modules/cnr-ibba/rsem/calculateexpression/** - -rsem/preparereference: - - modules/cnr-ibba/rsem/preparereference/** - - tests/modules/cnr-ibba/rsem/preparereference/** - -rseqc/bamstat: - - modules/cnr-ibba/rseqc/bamstat/** - - tests/modules/cnr-ibba/rseqc/bamstat/** - -rseqc/inferexperiment: - - modules/cnr-ibba/rseqc/inferexperiment/** - - tests/modules/cnr-ibba/rseqc/inferexperiment/** - -rseqc/innerdistance: - - modules/cnr-ibba/rseqc/innerdistance/** - - tests/modules/cnr-ibba/rseqc/innerdistance/** - -rseqc/junctionannotation: - - modules/cnr-ibba/rseqc/junctionannotation/** - - tests/modules/cnr-ibba/rseqc/junctionannotation/** - -rseqc/junctionsaturation: - - modules/cnr-ibba/rseqc/junctionsaturation/** - - tests/modules/cnr-ibba/rseqc/junctionsaturation/** - -rseqc/readdistribution: - - modules/cnr-ibba/rseqc/readdistribution/** - - tests/modules/cnr-ibba/rseqc/readdistribution/** - -rseqc/readduplication: - - modules/cnr-ibba/rseqc/readduplication/** - - tests/modules/cnr-ibba/rseqc/readduplication/** - -rseqc/tin: - - modules/cnr-ibba/rseqc/tin/** - - tests/modules/cnr-ibba/rseqc/tin/** - -rtgtools/pedfilter: - - modules/cnr-ibba/rtgtools/pedfilter/** - - tests/modules/cnr-ibba/rtgtools/pedfilter/** - -rtgtools/vcfeval: - - modules/cnr-ibba/rtgtools/vcfeval/** - - tests/modules/cnr-ibba/rtgtools/vcfeval/** - -salmon/index: - - modules/cnr-ibba/salmon/index/** - - tests/modules/cnr-ibba/salmon/index/** - -salmon/quant: - - modules/cnr-ibba/salmon/quant/** - - tests/modules/cnr-ibba/salmon/quant/** - -samblaster: - - modules/cnr-ibba/samblaster/** - - tests/modules/cnr-ibba/samblaster/** - -samtools/ampliconclip: - - modules/cnr-ibba/samtools/ampliconclip/** - - tests/modules/cnr-ibba/samtools/ampliconclip/** - -samtools/bam2fq: - - modules/cnr-ibba/samtools/bam2fq/** - - tests/modules/cnr-ibba/samtools/bam2fq/** - -samtools/calmd: - - modules/cnr-ibba/samtools/calmd/** - - tests/modules/cnr-ibba/samtools/calmd/** - -samtools/collate: - - modules/cnr-ibba/samtools/collate/** - - tests/modules/cnr-ibba/samtools/collate/** - -samtools/collatefastq: - - modules/cnr-ibba/samtools/collatefastq/** - - tests/modules/cnr-ibba/samtools/collatefastq/** - -samtools/convert: - - modules/cnr-ibba/samtools/convert/** - - tests/modules/cnr-ibba/samtools/convert/** - -samtools/coverage: - - modules/cnr-ibba/samtools/coverage/** - - tests/modules/cnr-ibba/samtools/coverage/** - -samtools/depth: - - modules/cnr-ibba/samtools/depth/** - - tests/modules/cnr-ibba/samtools/depth/** - -samtools/dict: - - modules/cnr-ibba/samtools/dict/** - - tests/modules/cnr-ibba/samtools/dict/** - -samtools/faidx: - - modules/cnr-ibba/samtools/faidx/** - - tests/modules/cnr-ibba/samtools/faidx/** - -samtools/fasta: - - modules/cnr-ibba/samtools/fasta/** - - tests/modules/cnr-ibba/samtools/fasta/** - -samtools/fastq: - - modules/cnr-ibba/samtools/fastq/** - - tests/modules/cnr-ibba/samtools/fastq/** - -samtools/fixmate: - - modules/cnr-ibba/samtools/fixmate/** - - tests/modules/cnr-ibba/samtools/fixmate/** - -samtools/flagstat: - - modules/cnr-ibba/samtools/flagstat/** - - tests/modules/cnr-ibba/samtools/flagstat/** - -samtools/getrg: - - modules/cnr-ibba/samtools/getrg/** - - tests/modules/cnr-ibba/samtools/getrg/** - -samtools/idxstats: - - modules/cnr-ibba/samtools/idxstats/** - - tests/modules/cnr-ibba/samtools/idxstats/** - -samtools/index: - - modules/cnr-ibba/samtools/index/** - - tests/modules/cnr-ibba/samtools/index/** - -samtools/markdup: - - modules/cnr-ibba/samtools/markdup/** - - tests/modules/cnr-ibba/samtools/markdup/** - -samtools/merge: - - modules/cnr-ibba/samtools/merge/** - - tests/modules/cnr-ibba/samtools/merge/** - -samtools/mpileup: - - modules/cnr-ibba/samtools/mpileup/** - - tests/modules/cnr-ibba/samtools/mpileup/** - -samtools/sort: - - modules/cnr-ibba/samtools/sort/** - - tests/modules/cnr-ibba/samtools/sort/** - -samtools/stats: - - modules/cnr-ibba/samtools/stats/** - - tests/modules/cnr-ibba/samtools/stats/** - -samtools/view: - - modules/cnr-ibba/samtools/view/** - - tests/modules/cnr-ibba/samtools/view/** - -scoary: - - modules/cnr-ibba/scoary/** - - tests/modules/cnr-ibba/scoary/** - -scramble/clusteranalysis: - - modules/cnr-ibba/scramble/clusteranalysis/** - - tests/modules/cnr-ibba/scramble/clusteranalysis/** - -scramble/clusteridentifier: - - modules/cnr-ibba/scramble/clusteridentifier/** - - tests/modules/cnr-ibba/scramble/clusteridentifier/** - -seacr/callpeak: - - modules/cnr-ibba/seacr/callpeak/** - - tests/modules/cnr-ibba/seacr/callpeak/** - -segemehl/align: - - modules/cnr-ibba/segemehl/align/** - - tests/modules/cnr-ibba/segemehl/align/** - -segemehl/index: - - modules/cnr-ibba/segemehl/index/** - - tests/modules/cnr-ibba/segemehl/index/** - -seqkit/pair: - - modules/cnr-ibba/seqkit/pair/** - - tests/modules/cnr-ibba/seqkit/pair/** - -seqkit/replace: - - modules/cnr-ibba/seqkit/replace/** - - tests/modules/cnr-ibba/seqkit/replace/** - -seqkit/rmdup: - - modules/cnr-ibba/seqkit/rmdup/** - - tests/modules/cnr-ibba/seqkit/rmdup/** - -seqkit/split2: - - modules/cnr-ibba/seqkit/split2/** - - tests/modules/cnr-ibba/seqkit/split2/** - -seqkit/stats: - - modules/cnr-ibba/seqkit/stats/** - - tests/modules/cnr-ibba/seqkit/stats/** - -seqsero2: - - modules/cnr-ibba/seqsero2/** - - tests/modules/cnr-ibba/seqsero2/** - -seqtk/mergepe: - - modules/cnr-ibba/seqtk/mergepe/** - - tests/modules/cnr-ibba/seqtk/mergepe/** - -seqtk/rename: - - modules/cnr-ibba/seqtk/rename/** - - tests/modules/cnr-ibba/seqtk/rename/** - -seqtk/sample: - - modules/cnr-ibba/seqtk/sample/** - - tests/modules/cnr-ibba/seqtk/sample/** - -seqtk/seq: - - modules/cnr-ibba/seqtk/seq/** - - tests/modules/cnr-ibba/seqtk/seq/** - -seqtk/subseq: - - modules/cnr-ibba/seqtk/subseq/** - - tests/modules/cnr-ibba/seqtk/subseq/** - -sequenzautils/bam2seqz: - - modules/cnr-ibba/sequenzautils/bam2seqz/** - - tests/modules/cnr-ibba/sequenzautils/bam2seqz/** - -sequenzautils/gcwiggle: - - modules/cnr-ibba/sequenzautils/gcwiggle/** - - tests/modules/cnr-ibba/sequenzautils/gcwiggle/** - -seqwish/induce: - - modules/cnr-ibba/seqwish/induce/** - - tests/modules/cnr-ibba/seqwish/induce/** - -seroba/run: - - modules/cnr-ibba/seroba/run/** - - tests/modules/cnr-ibba/seroba/run/** - -sexdeterrmine: - - modules/cnr-ibba/sexdeterrmine/** - - tests/modules/cnr-ibba/sexdeterrmine/** - -shasta: - - modules/cnr-ibba/shasta/** - - tests/modules/cnr-ibba/shasta/** - -shasum: - - modules/cnr-ibba/shasum/** - - tests/modules/cnr-ibba/shasum/** - -shigatyper: - - modules/cnr-ibba/shigatyper/** - - tests/modules/cnr-ibba/shigatyper/** - -shinyngs/app: - - modules/cnr-ibba/shinyngs/app/** - - tests/modules/cnr-ibba/shinyngs/app/** - -shinyngs/staticexploratory: - - modules/cnr-ibba/shinyngs/staticexploratory/** - - tests/modules/cnr-ibba/shinyngs/staticexploratory/** - -shovill: - - modules/cnr-ibba/shovill/** - - tests/modules/cnr-ibba/shovill/** - -sistr: - - modules/cnr-ibba/sistr/** - - tests/modules/cnr-ibba/sistr/** - -slimfastq: - - modules/cnr-ibba/slimfastq/** - - tests/modules/cnr-ibba/slimfastq/** - -snapaligner/align: - - modules/cnr-ibba/snapaligner/align/** - - tests/modules/cnr-ibba/snapaligner/align/** - -snapaligner/index: - - modules/cnr-ibba/snapaligner/index/** - - tests/modules/cnr-ibba/snapaligner/index/** - -snippy/core: - - modules/cnr-ibba/snippy/core/** - - tests/modules/cnr-ibba/snippy/core/** - -snippy/run: - - modules/cnr-ibba/snippy/run/** - - tests/modules/cnr-ibba/snippy/run/** - -snpdists: - - modules/cnr-ibba/snpdists/** - - tests/modules/cnr-ibba/snpdists/** - -snpeff: - - modules/cnr-ibba/snpeff/** - - tests/modules/cnr-ibba/snpeff/** - -snpsift/split: - - modules/cnr-ibba/snpsift/split/** - - tests/modules/cnr-ibba/snpsift/split/** - -snpsites: - - modules/cnr-ibba/snpsites/** - - tests/modules/cnr-ibba/snpsites/** - -somalier/extract: - - modules/cnr-ibba/somalier/extract/** - - tests/modules/cnr-ibba/somalier/extract/** - -somalier/relate: - - modules/cnr-ibba/somalier/relate/** - - tests/modules/cnr-ibba/somalier/relate/** - -sourmash/gather: - - modules/cnr-ibba/sourmash/gather/** - - tests/modules/cnr-ibba/sourmash/gather/** - -sourmash/sketch: - - modules/cnr-ibba/sourmash/sketch/** - - tests/modules/cnr-ibba/sourmash/sketch/** - -spades: - - modules/cnr-ibba/spades/** - - tests/modules/cnr-ibba/spades/** - -spatyper: - - modules/cnr-ibba/spatyper/** - - tests/modules/cnr-ibba/spatyper/** - -sratools/fasterqdump: - - modules/cnr-ibba/sratools/fasterqdump/** - - tests/modules/cnr-ibba/sratools/fasterqdump/** - -sratools/prefetch: - - modules/cnr-ibba/sratools/prefetch/** - - tests/modules/cnr-ibba/sratools/prefetch/** - -srst2/srst2: - - modules/cnr-ibba/srst2/srst2/** - - tests/modules/cnr-ibba/srst2/srst2/** - -ssuissero: - - modules/cnr-ibba/ssuissero/** - - tests/modules/cnr-ibba/ssuissero/** - -stadeniolib/scramble: - - modules/cnr-ibba/stadeniolib/scramble/** - - tests/modules/cnr-ibba/stadeniolib/scramble/** - -staphopiasccmec: - - modules/cnr-ibba/staphopiasccmec/** - - tests/modules/cnr-ibba/staphopiasccmec/** - -star/align: - - modules/cnr-ibba/star/align/** - - tests/modules/cnr-ibba/star/align/** - -star/genomegenerate: - - modules/cnr-ibba/star/genomegenerate/** - - tests/modules/cnr-ibba/star/genomegenerate/** - -stranger: - - modules/cnr-ibba/stranger/** - - tests/modules/cnr-ibba/stranger/** - -strelka/germline: - - modules/cnr-ibba/strelka/germline/** - - tests/modules/cnr-ibba/strelka/germline/** - -strelka/somatic: - - modules/cnr-ibba/strelka/somatic/** - - tests/modules/cnr-ibba/strelka/somatic/** - -stringtie/merge: - - modules/cnr-ibba/stringtie/merge/** - - tests/modules/cnr-ibba/stringtie/merge/** - -stringtie/stringtie: - - modules/cnr-ibba/stringtie/stringtie/** - - tests/modules/cnr-ibba/stringtie/stringtie/** - -subread/featurecounts: - - modules/cnr-ibba/subread/featurecounts/** - - tests/modules/cnr-ibba/subread/featurecounts/** - -subworkflows/align_bowtie2: - - subworkflows/cnr-ibba/align_bowtie2/** - - tests/subworkflows/cnr-ibba/align_bowtie2/** - -subworkflows/annotation/ensemblvep: - - subworkflows/cnr-ibba/annotation/ensemblvep/** - - tests/subworkflows/cnr-ibba/annotation/ensemblvep/** - -subworkflows/annotation/snpeff: - - subworkflows/cnr-ibba/annotation/snpeff/** - - tests/subworkflows/cnr-ibba/annotation/snpeff/** - -subworkflows/bam_dedup_stats_samtools_umitools: - - subworkflows/cnr-ibba/bam_dedup_stats_samtools_umitools/** - - tests/subworkflows/cnr-ibba/bam_dedup_stats_samtools_umitools/** - -subworkflows/bam_markduplicates_picard: - - subworkflows/cnr-ibba/bam_markduplicates_picard/** - - tests/subworkflows/cnr-ibba/bam_markduplicates_picard/** - -subworkflows/bam_qc_picard: - - subworkflows/cnr-ibba/bam_qc_picard/** - - tests/subworkflows/cnr-ibba/bam_qc_picard/** - -subworkflows/bam_rseqc: - - subworkflows/cnr-ibba/bam_rseqc/** - - tests/subworkflows/cnr-ibba/bam_rseqc/** - -subworkflows/bam_sort_samtools: - - subworkflows/cnr-ibba/bam_sort_samtools/** - - tests/subworkflows/cnr-ibba/bam_sort_samtools/** - -subworkflows/bam_sort_stats_samtools: - - subworkflows/cnr-ibba/bam_sort_stats_samtools/** - - tests/subworkflows/cnr-ibba/bam_sort_stats_samtools/** - -subworkflows/bam_stats_samtools: - - subworkflows/cnr-ibba/bam_stats_samtools/** - - tests/subworkflows/cnr-ibba/bam_stats_samtools/** - -subworkflows/bcl_demultiplex: - - subworkflows/cnr-ibba/bcl_demultiplex/** - - tests/subworkflows/cnr-ibba/bcl_demultiplex/** - -subworkflows/bedgraph_bedclip_bedgraphtobigwig: - - subworkflows/cnr-ibba/bedgraph_bedclip_bedgraphtobigwig/** - - tests/subworkflows/cnr-ibba/bedgraph_bedclip_bedgraphtobigwig/** - -subworkflows/fasta_index_dna: - - subworkflows/cnr-ibba/fasta_index_dna/** - - tests/subworkflows/cnr-ibba/fasta_index_dna/** - -subworkflows/fastq_align_dna: - - subworkflows/cnr-ibba/fastq_align_dna/** - - tests/subworkflows/cnr-ibba/fastq_align_dna/** - -subworkflows/fastq_align_hisat2: - - subworkflows/cnr-ibba/fastq_align_hisat2/** - - tests/subworkflows/cnr-ibba/fastq_align_hisat2/** - -subworkflows/fastq_contam_seqtk_kraken: - - subworkflows/cnr-ibba/fastq_contam_seqtk_kraken/** - - tests/subworkflows/cnr-ibba/fastq_contam_seqtk_kraken/** - -subworkflows/fastq_fastqc_umitools_trimgalore: - - subworkflows/cnr-ibba/fastq_fastqc_umitools_trimgalore/** - - tests/subworkflows/cnr-ibba/fastq_fastqc_umitools_trimgalore/** - -subworkflows/gatk_create_som_pon: - - subworkflows/cnr-ibba/gatk_create_som_pon/** - - tests/subworkflows/cnr-ibba/gatk_create_som_pon/** - -subworkflows/gatk_tumor_normal_somatic_variant_calling: - - subworkflows/cnr-ibba/gatk_tumor_normal_somatic_variant_calling/** - - tests/subworkflows/cnr-ibba/gatk_tumor_normal_somatic_variant_calling/** - -subworkflows/gatk_tumor_only_somatic_variant_calling: - - subworkflows/cnr-ibba/gatk_tumor_only_somatic_variant_calling/** - - tests/subworkflows/cnr-ibba/gatk_tumor_only_somatic_variant_calling/** - -subworkflows/homer/groseq: - - subworkflows/cnr-ibba/homer/groseq/** - - tests/subworkflows/cnr-ibba/homer/groseq/** - -subworkflows/srafastq: - - subworkflows/cnr-ibba/srafastq/** - - tests/subworkflows/cnr-ibba/srafastq/** - -svdb/merge: - - modules/cnr-ibba/svdb/merge/** - - tests/modules/cnr-ibba/svdb/merge/** - -svdb/query: - - modules/cnr-ibba/svdb/query/** - - tests/modules/cnr-ibba/svdb/query/** - -svtk/baftest: - - modules/cnr-ibba/svtk/baftest/** - - tests/modules/cnr-ibba/svtk/baftest/** - -svtk/countsvtypes: - - modules/cnr-ibba/svtk/countsvtypes/** - - tests/modules/cnr-ibba/svtk/countsvtypes/** - -svtk/rdtest2vcf: - - modules/cnr-ibba/svtk/rdtest2vcf/** - - tests/modules/cnr-ibba/svtk/rdtest2vcf/** - -svtk/standardize: - - modules/cnr-ibba/svtk/standardize/** - - tests/modules/cnr-ibba/svtk/standardize/** - -svtk/vcf2bed: - - modules/cnr-ibba/svtk/vcf2bed/** - - tests/modules/cnr-ibba/svtk/vcf2bed/** - -tabix/bgzip: - - modules/cnr-ibba/tabix/bgzip/** - - tests/modules/cnr-ibba/tabix/bgzip/** - -tabix/bgziptabix: - - modules/cnr-ibba/tabix/bgziptabix/** - - tests/modules/cnr-ibba/tabix/bgziptabix/** +seqkit/rmdup: + - modules/cnr-ibba/seqkit/rmdup/** + - tests/modules/cnr-ibba/seqkit/rmdup/** tabix/tabix: - - modules/cnr-ibba/tabix/tabix/** - - tests/modules/cnr-ibba/tabix/tabix/** - -tailfindr: - - modules/cnr-ibba/tailfindr/** - - tests/modules/cnr-ibba/tailfindr/** - -tbprofiler/profile: - - modules/cnr-ibba/tbprofiler/profile/** - - tests/modules/cnr-ibba/tbprofiler/profile/** - -tiddit/cov: - - modules/cnr-ibba/tiddit/cov/** - - tests/modules/cnr-ibba/tiddit/cov/** - -tiddit/sv: - - modules/cnr-ibba/tiddit/sv/** - - tests/modules/cnr-ibba/tiddit/sv/** - -transdecoder/longorf: - - modules/cnr-ibba/transdecoder/longorf/** - - tests/modules/cnr-ibba/transdecoder/longorf/** - -transdecoder/predict: - - modules/cnr-ibba/transdecoder/predict/** - - tests/modules/cnr-ibba/transdecoder/predict/** - -trimgalore: - - modules/cnr-ibba/trimgalore/** - - tests/modules/cnr-ibba/trimgalore/** - -trimmomatic: - - modules/cnr-ibba/trimmomatic/** - - tests/modules/cnr-ibba/trimmomatic/** - -ucsc/bedclip: - - modules/cnr-ibba/ucsc/bedclip/** - - tests/modules/cnr-ibba/ucsc/bedclip/** - -ucsc/bedgraphtobigwig: - - modules/cnr-ibba/ucsc/bedgraphtobigwig/** - - tests/modules/cnr-ibba/ucsc/bedgraphtobigwig/** - -ucsc/bedtobigbed: - - modules/cnr-ibba/ucsc/bedtobigbed/** - - tests/modules/cnr-ibba/ucsc/bedtobigbed/** - -ucsc/bigwigaverageoverbed: - - modules/cnr-ibba/ucsc/bigwigaverageoverbed/** - - tests/modules/cnr-ibba/ucsc/bigwigaverageoverbed/** - -ucsc/gtftogenepred: - - modules/cnr-ibba/ucsc/gtftogenepred/** - - tests/modules/cnr-ibba/ucsc/gtftogenepred/** - -ucsc/liftover: - - modules/cnr-ibba/ucsc/liftover/** - - tests/modules/cnr-ibba/ucsc/liftover/** - -ucsc/wigtobigwig: - - modules/cnr-ibba/ucsc/wigtobigwig/** - - tests/modules/cnr-ibba/ucsc/wigtobigwig/** - -ultra/align: - - modules/cnr-ibba/ultra/align/** - - tests/modules/cnr-ibba/ultra/align/** - -ultra/index: - - modules/cnr-ibba/ultra/index/** - - tests/modules/cnr-ibba/ultra/index/** - -ultra/pipeline: - - modules/cnr-ibba/ultra/pipeline/** - - tests/modules/cnr-ibba/ultra/pipeline/** - -umitools/dedup: - - modules/cnr-ibba/umitools/dedup/** - - modules/cnr-ibba/umitools/extract/** - - tests/modules/cnr-ibba/umitools/dedup/** - -umitools/extract: - - modules/cnr-ibba/umitools/extract/** - - tests/modules/cnr-ibba/umitools/extract/** - -unicycler: - - modules/cnr-ibba/unicycler/** - - tests/modules/cnr-ibba/unicycler/** - -untar: - - modules/cnr-ibba/untar/** - - tests/modules/cnr-ibba/untar/** - -unzip: - - modules/cnr-ibba/unzip/** - - tests/modules/cnr-ibba/unzip/** - -vardictjava: - - modules/cnr-ibba/vardictjava/** - - tests/modules/cnr-ibba/vardictjava/** - -variantbam: - - modules/cnr-ibba/variantbam/** - - tests/modules/cnr-ibba/variantbam/** - -vcf2db: - - modules/cnr-ibba/vcf2db/** - - tests/modules/cnr-ibba/vcf2db/** - -vcf2maf: - - modules/cnr-ibba/vcf2maf/** - - tests/modules/cnr-ibba/vcf2maf/** - -vcfanno: - - modules/cnr-ibba/vcfanno/** - - tests/modules/cnr-ibba/vcfanno/** - -vcflib/vcfbreakmulti: - - modules/cnr-ibba/vcflib/vcfbreakmulti/** - - tests/modules/cnr-ibba/vcflib/vcfbreakmulti/** - -vcflib/vcfuniq: - - modules/cnr-ibba/vcflib/vcfuniq/** - - tests/modules/cnr-ibba/vcflib/vcfuniq/** - -vcftools: - - modules/cnr-ibba/vcftools/** - - tests/modules/cnr-ibba/vcftools/** - -verifybamid/verifybamid2: - - modules/cnr-ibba/verifybamid/verifybamid2/** - - tests/modules/cnr-ibba/verifybamid/verifybamid2/** - -vg/deconstruct: - - modules/cnr-ibba/vg/deconstruct/** - - tests/modules/cnr-ibba/vg/deconstruct/** - -vsearch/cluster: - - modules/cnr-ibba/vsearch/cluster/** - - tests/modules/cnr-ibba/vsearch/cluster/** - -vsearch/sintax: - - modules/cnr-ibba/vsearch/sintax/** - - tests/modules/cnr-ibba/vsearch/sintax/** - -vsearch/usearchglobal: - - modules/cnr-ibba/vsearch/usearchglobal/** - - tests/modules/cnr-ibba/vsearch/usearchglobal/** - -wgsim: - - modules/cnr-ibba/wgsim/** - - tests/modules/cnr-ibba/wgsim/** - -whamg: - - modules/cnr-ibba/whamg/** - - tests/modules/cnr-ibba/whamg/** - -yara/index: - - modules/cnr-ibba/yara/index/** - - tests/modules/cnr-ibba/yara/index/** - -yara/mapper: - - modules/cnr-ibba/yara/mapper/** - - tests/modules/cnr-ibba/yara/mapper/** + - modules/nf-core/tabix/tabix/** + - tests/modules/nf-core/tabix/tabix/** From 3b3c287ef943a702c7f56186c702c98c8860da8c Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 14:48:59 +0100 Subject: [PATCH 03/14] :white_check_mark: fix tests --- tests/modules/nf-core/bcftools/concat/test.yml | 4 ++-- tests/modules/nf-core/samtools/coverage/main.nf | 2 +- tests/modules/nf-core/samtools/coverage/test.yml | 2 +- tests/modules/nf-core/samtools/flagstat/test.yml | 2 +- tests/modules/nf-core/samtools/idxstats/test.yml | 2 +- tests/modules/nf-core/samtools/stats/test.yml | 4 ++-- tests/modules/nf-core/tabix/tabix/test.yml | 12 ++++++------ .../{cnr-ibba => nf-core}/bam_stats_samtools/main.nf | 2 +- .../bam_stats_samtools/nextflow.config | 0 .../bam_stats_samtools/test.yml | 6 +++--- 10 files changed, 18 insertions(+), 18 deletions(-) rename tests/subworkflows/{cnr-ibba => nf-core}/bam_stats_samtools/main.nf (93%) rename tests/subworkflows/{cnr-ibba => nf-core}/bam_stats_samtools/nextflow.config (100%) rename tests/subworkflows/{cnr-ibba => nf-core}/bam_stats_samtools/test.yml (76%) diff --git a/tests/modules/nf-core/bcftools/concat/test.yml b/tests/modules/nf-core/bcftools/concat/test.yml index 016927b..dd0fa4c 100644 --- a/tests/modules/nf-core/bcftools/concat/test.yml +++ b/tests/modules/nf-core/bcftools/concat/test.yml @@ -1,5 +1,5 @@ - name: bcftools concat test_bcftools_concat_tbi - command: nextflow run ./tests/modules/cnr-ibba/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/bcftools/concat/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/concat/nextflow.config tags: - bcftools - bcftools/concat @@ -8,7 +8,7 @@ md5sum: 18c1612343f5e8a219ee6476a870a674 - name: bcftools concat test_bcftools_concat_no_tbi - command: nextflow run ./tests/modules/cnr-ibba/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/bcftools/concat/nextflow.config + command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/concat/nextflow.config tags: - bcftools - bcftools/concat diff --git a/tests/modules/nf-core/samtools/coverage/main.nf b/tests/modules/nf-core/samtools/coverage/main.nf index 0e346dc..4617944 100644 --- a/tests/modules/nf-core/samtools/coverage/main.nf +++ b/tests/modules/nf-core/samtools/coverage/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COVERAGE } from '../../../../../modules/cnr-ibba/samtools/coverage/main.nf' +include { SAMTOOLS_COVERAGE } from '../../../../../modules/nf-core/samtools/coverage/main.nf' workflow test_samtools_coverage { diff --git a/tests/modules/nf-core/samtools/coverage/test.yml b/tests/modules/nf-core/samtools/coverage/test.yml index 2f2d1fd..5e62fe9 100644 --- a/tests/modules/nf-core/samtools/coverage/test.yml +++ b/tests/modules/nf-core/samtools/coverage/test.yml @@ -1,5 +1,5 @@ - name: samtools coverage test_samtools_coverage - command: nextflow run ./tests/modules/cnr-ibba/samtools/coverage -entry test_samtools_coverage -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/samtools/coverage/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/coverage -entry test_samtools_coverage -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/coverage/nextflow.config tags: - samtools/coverage - samtools diff --git a/tests/modules/nf-core/samtools/flagstat/test.yml b/tests/modules/nf-core/samtools/flagstat/test.yml index 3dc63cc..ad58ad5 100644 --- a/tests/modules/nf-core/samtools/flagstat/test.yml +++ b/tests/modules/nf-core/samtools/flagstat/test.yml @@ -1,5 +1,5 @@ - name: samtools flagstat test_samtools_flagstat - command: nextflow run ./tests/modules/cnr-ibba/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/samtools/flagstat/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/flagstat/nextflow.config tags: - samtools/flagstat - samtools diff --git a/tests/modules/nf-core/samtools/idxstats/test.yml b/tests/modules/nf-core/samtools/idxstats/test.yml index 6a9f1ed..8c596c2 100644 --- a/tests/modules/nf-core/samtools/idxstats/test.yml +++ b/tests/modules/nf-core/samtools/idxstats/test.yml @@ -1,5 +1,5 @@ - name: samtools idxstats test_samtools_idxstats - command: nextflow run ./tests/modules/cnr-ibba/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/samtools/idxstats/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/idxstats/nextflow.config tags: - samtools/idxstats - samtools diff --git a/tests/modules/nf-core/samtools/stats/test.yml b/tests/modules/nf-core/samtools/stats/test.yml index a5aa006..819db89 100644 --- a/tests/modules/nf-core/samtools/stats/test.yml +++ b/tests/modules/nf-core/samtools/stats/test.yml @@ -1,5 +1,5 @@ - name: samtools stats test_samtools_stats - command: nextflow run ./tests/modules/cnr-ibba/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/samtools/stats/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/stats/nextflow.config tags: - samtools - samtools/stats @@ -8,7 +8,7 @@ md5sum: 37b24a161ade89aef4155df6354efa8c - name: samtools stats test_samtools_stats_cram - command: nextflow run ./tests/modules/cnr-ibba/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/samtools/stats/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/stats/nextflow.config tags: - samtools - samtools/stats diff --git a/tests/modules/nf-core/tabix/tabix/test.yml b/tests/modules/nf-core/tabix/tabix/test.yml index 7d52d57..5a2fb2d 100644 --- a/tests/modules/nf-core/tabix/tabix/test.yml +++ b/tests/modules/nf-core/tabix/tabix/test.yml @@ -1,5 +1,5 @@ - name: tabix tabix bed - command: nextflow run ./tests/modules/cnr-ibba/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix @@ -7,7 +7,7 @@ - path: ./output/tabix/test.bed.gz.tbi md5sum: 5b40851ab6b8ccf7946313c86481c0df - name: tabix tabix gff - command: nextflow run ./tests/modules/cnr-ibba/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix @@ -15,18 +15,18 @@ - path: ./output/tabix/genome.gff3.gz.tbi md5sum: f79a67d95a98076e04fbe0455d825926 - name: tabix tabix vcf - command: nextflow run ./tests/modules/cnr-ibba/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix files: - path: output/tabix/test.vcf.gz.tbi - md5sum: 36e11bf96ed0af4a92caa91a68612d64 + md5sum: d22e5b84e4fcd18792179f72e6da702e - name: tabix tabix vcf csi - command: nextflow run ./tests/modules/cnr-ibba/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/tabix/tabix/nextflow.config + command: nextflow run ./tests/modules/nf-core/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config tags: - tabix - tabix/tabix files: - path: output/tabix/test.vcf.gz.csi - md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd + md5sum: 6f733d80ee760fcc8fdbe504a03f2640 diff --git a/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf b/tests/subworkflows/nf-core/bam_stats_samtools/main.nf similarity index 93% rename from tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf rename to tests/subworkflows/nf-core/bam_stats_samtools/main.nf index 07525ab..14884fb 100644 --- a/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf +++ b/tests/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAM_STATS_SAMTOOLS } from '../../../../subworkflows/cnr-ibba/bam_stats_samtools/main' +include { BAM_STATS_SAMTOOLS } from '../../../../subworkflows/nf-core/bam_stats_samtools/main' workflow test_bam_stats_samtools_single_end { input = [ diff --git a/tests/subworkflows/cnr-ibba/bam_stats_samtools/nextflow.config b/tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config similarity index 100% rename from tests/subworkflows/cnr-ibba/bam_stats_samtools/nextflow.config rename to tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config diff --git a/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml similarity index 76% rename from tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml rename to tests/subworkflows/nf-core/bam_stats_samtools/test.yml index 74cc014..1325c61 100644 --- a/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml +++ b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml @@ -1,5 +1,5 @@ - name: bam_stats_samtools test_bam_stats_samtools_single_end - command: nextflow run ./tests/subworkflows/cnr-ibba/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c ./tests/config/nextflow.config + command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c ./tests/config/nextflow.config tags: - samtools - samtools/flagstat @@ -16,7 +16,7 @@ md5sum: 930cf4e764cfa0ee4f3ca0168442f338 - name: bam_stats_samtools test_bam_stats_samtools_paired_end - command: nextflow run ./tests/subworkflows/cnr-ibba/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c ./tests/config/nextflow.config + command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c ./tests/config/nextflow.config tags: - samtools - samtools/flagstat @@ -33,7 +33,7 @@ md5sum: 7602d5fc2bc0207cca3f6ee214d1688f - name: bam_stats_samtools test_bam_stats_samtools_paired_end_cram - command: nextflow run ./tests/subworkflows/cnr-ibba/bam_stats_samtools -entry test_bam_stats_samtools_paired_end_cram -c ./tests/config/nextflow.config + command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end_cram -c ./tests/config/nextflow.config tags: - samtools - samtools/flagstat From 0907c9b081e457c6817f53e684d69d2a12de65ef Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 15:31:16 +0100 Subject: [PATCH 04/14] :wrench: update test configs --- tests/config/nextflow.config | 23 +- tests/config/nf-test.config | 50 ++ tests/config/test_data.config | 1121 ++++++++++++++++++++------------- 3 files changed, 742 insertions(+), 452 deletions(-) create mode 100644 tests/config/nf-test.config diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 98b9eed..c24e252 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -1,8 +1,8 @@ params { outdir = "output/" publish_dir_mode = "copy" - enable_conda = false singularity_pull_docker_container = false + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' } process { @@ -15,14 +15,25 @@ if ("$PROFILE" == "singularity") { singularity.enabled = true singularity.autoMounts = true } else if ("$PROFILE" == "conda") { - params.enable_conda = true - conda.enabled=true + conda.enabled = true +} else if ("$PROFILE" == "mamba") { + conda.enabled = true + conda.useMamba = true +} else if ("$PROFILE" == "podman") { + podman.enabled = true + podman.userEmulation = true + podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" } else { docker.enabled = true - docker.userEmulation = true - docker.runOptions = "--platform linux/x86_64" + docker.userEmulation = false + docker.fixOwnership = true + docker.runOptions = '--platform=linux/amd64' } +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + // Increase time available to build Conda environment conda { createTimeout = "120 min" } @@ -30,5 +41,5 @@ conda { createTimeout = "120 min" } includeConfig 'test_data.config' manifest { - nextflowVersion = '!>=21.10.0' + nextflowVersion = '!>=23.04.0' } diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config new file mode 100644 index 0000000..a37850f --- /dev/null +++ b/tests/config/nf-test.config @@ -0,0 +1,50 @@ +params { + publish_dir_mode = "copy" + singularity_pull_docker_container = false + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' +} + +process { + cpus = 2 + memory = 3.GB + time = 2.h +} + +profiles { + singularity { + singularity.enabled = true + singularity.autoMounts = true + } + conda { + conda.enabled = true + } + mamba { + conda.enabled = true + conda.useMamba = true + } + podman { + podman.enabled = true + podman.userEmulation = true + podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" + } + docker { + docker.enabled = true + docker.userEmulation = false + docker.fixOwnership = true + docker.runOptions = '--platform=linux/amd64' + } +} + +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Increase time available to build Conda environment +conda { createTimeout = "120 min" } + +// Load test_data.config containing paths to test data +includeConfig 'test_data.config' + +manifest { + nextflowVersion = '!>=23.04.0' +} diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 69550e4..93347cf 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -1,526 +1,755 @@ -// Base directory for test data -def test_data_dir = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data" +// README: +// https://github.com/nf-core/test-datasets/blob/modules/README.md params { + // Base directory for test data + test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" + test_data { 'sarscov2' { 'genome' { - genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta" - genome_fasta_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.gz" - genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai" - genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict" - genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3" - genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz" - genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf" - genome_paf = "${test_data_dir}/genomics/sarscov2/genome/genome.paf" - genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes" - transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta" - proteome_fasta = "${test_data_dir}/genomics/sarscov2/genome/proteome.fasta" - transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf" - - test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed" - test_bed_gz = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed.gz" - test2_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test2.bed" - test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12" - baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed" - bed_autosql = "${test_data_dir}/genomics/sarscov2/genome/bed/bed6alt.as" - - reference_cnn = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn" - - kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2" - kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz" - - kraken2_bracken = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken" - kraken2_bracken_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" - - kaiju = "${test_data_dir}/genomics/sarscov2/genome/db/kaiju" - kaiju_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kaiju.tar.gz" - - kofamscan_profiles_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz" - kofamscan_ko_list_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kofamscan/ko_list.gz" - - ncbi_taxmap_zip = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip" - taxon_list_txt = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt" - - all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas" - informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas" - - contigs_genome_maf_gz = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz" - contigs_genome_par = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.par" - lastdb_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz" - - baits_interval_list = "${test_data_dir}/genomics/sarscov2/genome/picard/baits.interval_list" - targets_interval_list = "${test_data_dir}/genomics/sarscov2/genome/picard/targets.interval_list" + genome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta" + genome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz" + genome_fasta_fai = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai" + genome_fasta_txt_zst = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.txt.zst" + genome_dict = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.dict" + genome_gff3 = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3" + genome_gff3_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz" + genome_gtf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gtf" + genome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.paf" + genome_sizes = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.sizes" + transcriptome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta" + transcriptome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf" + proteome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta" + proteome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta.gz" + + test_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed" + test_bed_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz" + test2_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed" + test_bed12 = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12" + baits_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed" + bed_autosql = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as" + + reference_cnn = "${params.test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn" + + kraken2 = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2" + kraken2_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz" + + kraken2_bracken = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken" + kraken2_bracken_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" + + kaiju = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju" + kaiju_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz" + + kofamscan_profiles_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz" + kofamscan_ko_list_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz" + + ncbi_taxmap_zip = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip" + taxon_list_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt" + + mmseqs_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz" + + all_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas" + informative_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas" + + contigs_genome_maf_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz" + contigs_genome_par = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par" + lastdb_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz" + + baits_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list" + targets_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list" + regions_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt" + lc_extrap_mr = "${params.test_data_base}/data/delete_me/preseq/SRR1003759_5M_subset.mr" } 'illumina' { - test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.bam" - test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" - test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" - test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.bam" - test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" - test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" - test_paired_end_methylated_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" - test_paired_end_methylated_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam" - test_paired_end_methylated_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai" - test_unaligned_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.unaligned.bam" - - test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" - test_interleaved_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz" - test2_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" - test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz" - test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz" - - test_bedgraph = "${test_data_dir}/genomics/sarscov2/illumina/bedgraph/test.bedgraph" - - test_bigwig = "${test_data_dir}/genomics/sarscov2/illumina/bigwig/test.bigwig" - - test_wig_gz = "${test_data_dir}/genomics/sarscov2/illumina/wig/test.wig.gz" - - test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" - - test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" - - test_bcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf" - - test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf" - test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz" - test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" - test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf" - test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz" - test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" - test2_vcf_targets_tsv_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz" - test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf" - test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz" - test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" - - contigs_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/contigs.fasta" - scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta" - - assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa" - assembly_gfa_bgz = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz" - assembly_gfa_gz = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.gz" - assembly_gfa_zst = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.zst" - - test_single_end_bam_readlist_txt = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt" - - SRR13255544_tar_gz = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" - SRR11140744_tar_gz = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" + test_single_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam" + test_single_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" + test_single_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" + test_paired_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" + test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_methylated_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" + test_paired_end_methylated_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam" + test_paired_end_methylated_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai" + test_unaligned_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam" + + test_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" + test_interleaved_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz" + test_1_fastq_txt_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" + test_methylated_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz" + test_methylated_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz" + test_1_fastq_gz_fastqc_html = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.html" + test_1_fastq_gz_fastqc_zip = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" + + test_bedgraph = "${params.test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph" + + test_bigwig = "${params.test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig" + + test_wig_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz" + + test_baserecalibrator_table = "${params.test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" + + test_computematrix_mat_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" + + test_bcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf" + + test_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf" + test_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz" + test_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" + test2_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf" + test2_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" + test2_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" + test2_vcf_targets_tsv_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz" + test3_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf" + test3_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz" + test3_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" + + contigs_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta" + scaffolds_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" + + assembly_gfa = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa" + assembly_gfa_bgz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz" + assembly_gfa_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz" + assembly_gfa_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst" + + test_single_end_bam_readlist_txt = "${params.test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt" + + SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" + SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" } 'nanopore' { - test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam" - test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" + test_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam" + test_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" - fast5_tar_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fast5/fast5.tar.gz" + fast5_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz" - test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz" + test_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz" - test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" + test_sequencing_summary = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" } 'metagenome' { - classified_reads_assignment = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" - kraken_report = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" - krona_taxonomy = "${test_data_dir}/genomics/sarscov2/metagenome/krona_taxonomy.tab" - seqid2taxid_map = "${test_data_dir}/genomics/sarscov2/metagenome/seqid2taxid.map" + classified_reads_assignment = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" + kraken_report = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" + krona_taxonomy = "${params.test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab" + seqid2taxid_map = "${params.test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map" + nodes_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/nodes.dmp" + names_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/names.dmp" + prot_nodes_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_nodes.dmp" + prot_names_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_names.dmp" + prot_accession2taxid_gz = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot.accession2taxid.gz" } } 'mus_musculus' { 'genome' { - rnaseq_samplesheet = "${test_data_dir}/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv" - rnaseq_genemeta = "${test_data_dir}/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv" - rnaseq_contrasts = "${test_data_dir}/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv" - rnaseq_matrix = "${test_data_dir}/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv" - deseq_results = "${test_data_dir}/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv" + rnaseq_samplesheet = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv" + rnaseq_genemeta = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv" + rnaseq_contrasts = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv" + rnaseq_matrix = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv" + rnaseq_lengths = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv" + deseq_results = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv" + } + 'illumina' { + test_1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz" + } + 'csv' { + count_table = "${params.test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv" + library = "${params.test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv" + } + 'txt' { + design_matrix = "${params.test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt" } } 'homo_sapiens' { + '10xgenomics' { + cellranger { + test_10x_10k_pbmc_5fb_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5fb_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv" + + test_10x_10k_pbmc_cmo_cmo_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_cmo_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/10k_pbmc_cmo_count_feature_reference.csv" + + test_10x_5k_cmvpos_tcells_ab_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_ab_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv" + + test_10x_vdj_ref_json = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json" + test_10x_vdj_ref_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa" + test_10x_vdj_ref_suppfasta = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa" + + test_scATAC_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R1_001.fastq.gz" + test_scATAC_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R2_001.fastq.gz" + test_scATAC_3_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R3_001.fastq.gz" + test_scATAC_I_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_I1_001.fastq.gz" + } + spaceranger { + test_10x_ffpe_cytassist_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_cytassist_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_cytassist_image = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif" + test_10x_ffpe_cytassist_probeset = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv" + + test_10x_ffpe_v1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_v1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_v1_image = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" + } + } 'genome' { - genome_elfasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elfasta" - genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta" - genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai" - genome_strtablefile = "${test_data_dir}/genomics/homo_sapiens/genome/genome_strtablefile.zip" - genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict" - genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3" - genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf" - genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list" - genome_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.multi_intervals.bed" - genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes" - genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed" - genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header" - genome_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz" - genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi" - genome_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elsites" - transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta" - genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta" - genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz" - genome_21_sdf = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz" - genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" - genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" - genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" - genome_21_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" - genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" - genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" - genome_21_multi_interval_antitarget_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed" - genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" - genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" - genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" - genome_21_reference_cnn = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" - - dbsnp_146_hg38_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" - dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" - dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" - gnomad_r2_1_1_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" - gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" - mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" - mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" - syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" - syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" - syntheticvcf_short_score = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score" - gnomad_r2_1_1_sv_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" - gnomad2_r2_1_1_sv_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz" - - hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" - hapmap_3_3_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" - res_1000g_omni2_5_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" - res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" - res_1000g_phase1_snps_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" - res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" - dbsnp_138_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" - dbsnp_138_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - gnomad_r2_1_1_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" - gnomad_r2_1_1_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" - mills_and_1000g_indels_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" - mills_and_1000g_indels_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" - haplotype_map = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" - - index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon" - repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json" - justhusky_ped = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" - justhusky_minimal_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" - justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" - - vcfanno_tar_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" - vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" - - vep_cache = "${test_data_dir}/genomics/homo_sapiens/genome/vep.tar.gz" + genome_elfasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta" + genome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta" + genome_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" + genome_fasta_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz" + genome_fasta_gz_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.fai" + genome_fasta_gz_gzi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.gzi" + genome_strtablefile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip" + genome_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict" + genome_gff3 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3" + genome_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf" + genome_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list" + genome_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed" + genome_blacklist_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed" + genome_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes" + genome_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed" + genome_header = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.header" + genome_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz" + genome_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi" + genome_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites" + transcriptome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta" + genome2_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta" + genome_chain_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz" + genome_annotated_interval_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv" + genome_mt_gb = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.NC_012920_1.gb" + genome_preprocessed_count_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv" + genome_preprocessed_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list" + genome_ploidy_model = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_model.tar.gz" + genome_ploidy_calls = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_calls.tar.gz" + genome_germline_cnv_model = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_model.tar.gz" + genome_germline_cnv_calls = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_calls.tar.gz" + genome_motifs = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_motifs.txt" + genome_config = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_config.json" + + genome_1_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.fasta.gz" + genome_1_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.gtf" + + genome_21_sdf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz" + genome_21_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + genome_21_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + genome_21_gencode_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf" + genome_21_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" + genome_21_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" + genome_21_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" + genome_21_annotated_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed" + genome_21_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + genome_21_multi_interval_antitarget_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed" + genome_21_multi_interval_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" + genome_21_multi_interval_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" + genome_21_chromosomes_dir = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + genome_21_reference_cnn = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" + genome_21_eigenstrat_snp = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp" + genome_21_stitch_posfile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/dbsnp_138.hg38.first_10_biallelic_sites.tsv" + + dbsnp_146_hg38_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" + dbsnp_146_hg38_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_146_hg38_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + gnomad_r2_1_1_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + mills_and_1000g_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + syntheticvcf_short_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" + syntheticvcf_short_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" + syntheticvcf_short_score = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score" + gnomad_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" + gnomad2_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz" + + hapmap_3_3_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" + hapmap_3_3_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" + res_1000g_omni2_5_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" + res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" + res_1000g_phase1_snps_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" + res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" + dbsnp_138_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_138_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + gnomad_r2_1_1_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + mills_and_1000g_indels_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + haplotype_map = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" + dbNSFP_4_1a_21_hg38_txt_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz" + dbNSFP_4_1a_21_hg38_txt_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi" + ngscheckmate_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" + + index_salmon = "${params.test_data_base}/data/genomics/homo_sapiens/genome/index/salmon" + repeat_expansions = "${params.test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json" + justhusky_ped = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" + justhusky_minimal_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" + justhusky_minimal_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" + + vcfanno_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" + vcfanno_toml = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" + updsites_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/updsites.bed" + + prg_input = "${params.test_data_base}/data/genomics/homo_sapiens/genome/PRG_test.zip" + crispr_functional_counts = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/functional_genomics_counts.tsv" + crispr_functional_library = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/library_functional_genomics.tsv" + + vep_cache = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz" + affy_array_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751.csv" + affy_array_celfiles_tar = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751_RAW.tar" + } 'pangenome' { - pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa" - pangenome_fa_bgzip = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz" - pangenome_fa_bgzip_fai = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz.fai" - pangenome_fa_bgzip_gzi = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz.gzi" - pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf" - pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz" - pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa" - pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" - pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" + pangenome_fa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa" + pangenome_fa_bgzip = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz" + pangenome_fa_bgzip_fai = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai" + pangenome_fa_bgzip_gzi = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi" + pangenome_paf = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf" + pangenome_paf_gz = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz" + pangenome_panacus_tsv = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.panacus.tsv" + pangenome_seqwish_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa" + pangenome_smoothxg_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" + pangenome_gfaffix_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" 'odgi' { - pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og" - pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay" + pangenome_og = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og" + pangenome_lay = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay" } } 'illumina' { - test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" - test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" - test_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam" - test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" - test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" - test_paired_end_markduplicates_sorted_referencesn_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt" - test_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" - test_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" - test_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" - test_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" - test_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" - test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" - test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" - test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" - test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" - test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" - test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" - test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" - test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" - test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" - test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" - test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" - test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" - test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" - test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" - test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" - test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" - test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" - test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" - test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" - test_paired_end_duplex_umi_unmapped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam" - test_paired_end_duplex_umi_mapped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam" - test_paired_end_duplex_umi_mapped_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam" - test_paired_end_duplex_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam" - test_paired_end_duplex_umi_duplex_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam" - - mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" - mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" - - test3_single_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam" - - read_group_settings_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/read_group_settings.txt" - - test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" - test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" - test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" - test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" - test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" - test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" - - test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" - test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" - test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" - test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" - test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" - test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" - - test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" - test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" - test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" - test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" - test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" - test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" - test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" - test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" - test_paired_end_duplex_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz" - test_paired_end_duplex_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz" - - test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" - test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" - test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table" - test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" - - test_paired_end_sorted_dragstrmodel = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt" - - test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" - test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" - - test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" - test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" - test_haplotc_cnn_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" - test_haplotc_cnn_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" - - test2_haplotc_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" - test2_haplotc_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" - - test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" - test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" - test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" - test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" - test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" - test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" - - test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" - test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" - test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" - test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" - test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" - test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" - test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" - - test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" - test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" - test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" - test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" - - test_genome_vcf_ud = "${test_data_dir}/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD" - test_genome_vcf_mu = "${test_data_dir}/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu" - test_genome_vcf_bed = "${test_data_dir}/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed" - - test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" - test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" - test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" - test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" - - test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" - test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" - - test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" - test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" - - test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" - test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" - - test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" - test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" - - test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz" - test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz" - - test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak" - test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak" - - cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" - cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" - - test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" - test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" - genmod_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz" - genmod_annotate_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz" - genmod_models_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz" - genmod_score_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz" - - test_mito_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz" - - test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor" - rank_model = "${test_data_dir}/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini" - - test_flowcell = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" - test_flowcell_samplesheet = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv" - + test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam" + test_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" + test_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" + test_paired_end_markduplicates_sorted_referencesn_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt" + test_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" + test_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" + test_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" + test_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" + test_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" + test_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" + test_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" + test_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" + test_paired_end_hla = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" + test_paired_end_hla_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" + test_paired_end_hla_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" + test_rna_paired_end_sorted_chr6_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam" + test_rna_paired_end_sorted_chr6_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai" + + test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" + test2_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" + test2_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" + test2_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" + test2_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" + test2_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" + test2_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" + test2_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" + test2_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" + test2_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" + test2_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" + test2_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" + test_paired_end_duplex_umi_unmapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam" + test_paired_end_duplex_umi_mapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam" + test_paired_end_duplex_umi_mapped_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam" + test_paired_end_duplex_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam" + test_paired_end_duplex_umi_duplex_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam" + + mitochon_standin_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" + mitochon_standin_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" + test_illumina_mt_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam" + test_illumina_mt_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai" + + test3_single_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam" + + read_group_settings_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt" + + test_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" + test_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" + test_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" + test_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" + test_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" + test_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" + + test2_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" + test2_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" + test2_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" + test2_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" + test2_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" + test2_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" + test3_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram" + test3_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram.crai" + + test_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" + test_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" + test_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" + test_airrseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz" + test_airrseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" + test2_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" + test2_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" + test_rnaseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" + test_rnaseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" + test_paired_end_duplex_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz" + test_paired_end_duplex_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz" + + test_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" + test2_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" + test_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table" + test2_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" + + test_paired_end_sorted_dragstrmodel = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt" + + test_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" + test_pon_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" + + test2_haplotc_ann_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" + test2_haplotc_ann_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + test_haplotc_cnn_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" + test_haplotc_cnn_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" + + test2_haplotc_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" + test2_haplotc_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" + + test2_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" + test2_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" + test2_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" + test2_allele_specific_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" + test2_allele_specific_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" + test2_allele_specific_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" + + test_test2_paired_mutect2_calls_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" + test_test2_paired_mutect2_calls_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" + test_test2_paired_mutect2_calls_vcf_gz_stats = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" + test_test2_paired_mutect2_calls_f1r2_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" + test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" + test_test2_paired_segmentation_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" + test_test2_paired_contamination_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" + + test_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" + test_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" + test_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" + test_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" + + test_genome_vcf_ud = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD" + test_genome_vcf_mu = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu" + test_genome_vcf_bed = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed" + + test2_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" + test2_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" + test2_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" + test2_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" + + test_genome21_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" + test_genome21_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + + test_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" + test2_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" + + test_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" + test2_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" + + test_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" + test2_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" + + test_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak" + test2_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak" + + cutandrun_bedgraph_test_1 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" + cutandrun_bedgraph_test_2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" + na24385_chr22_coverage = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/NA24385_coverage.bed" + + empty_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz" + empty_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz.tbi" + + simulated_sv = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz" + simulated_sv_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz.tbi" + simulated_sv2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz" + simulated_sv2_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz.tbi" + + test_rnaseq_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" + test_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" + test_sv_vcf_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi" + na24385_chr22_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz" + na24385_chr22_sv_vcf_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi" + genmod_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz" + genmod_annotate_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz" + genmod_models_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz" + genmod_score_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz" + + test_mito_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz" + + test_pytor = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor" + rank_model = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini" + + test_flowcell = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" + test_flowcell_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv" + + varlociraptor_scenario = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml" + + contig_ploidy_priors_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" + + purecn_ex1_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam" + purecn_ex1_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai" + purecn_ex1_interval = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt" + purecn_ex1_normal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_normal.txt.gz" + purecn_ex2_normal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex2_normal.txt.gz" + purecn_normalpanel_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz" + purecn_normalpanel_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi" } 'pacbio' { - primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta" - alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam" - alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" - ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" - ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" - ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" - ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" - ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" - ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" - hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" - lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" - refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" - cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" - singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" - aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" - alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" - genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" - genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" - filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt" + primers = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta" + alz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam" + alzpbi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" + ccs = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" + ccs_fa = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" + ccs_fa_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" + ccs_fq = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" + ccs_fq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" + ccs_xml = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" + hifi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" + lima = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" + refine = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" + cluster = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" + singletons = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" + aligned = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" + alignedbai = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" + genemodel1 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" + genemodel2 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" + filelist = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt" } 'scramble' { - fasta = "${test_data_dir}/genomics/homo_sapiens/scramble/test.fa" - fasta_fai = "${test_data_dir}/genomics/homo_sapiens/scramble/test.fa.fai" - bam = "${test_data_dir}/genomics/homo_sapiens/scramble/test.bam" - bam_bai = "${test_data_dir}/genomics/homo_sapiens/scramble/test.bam.bai" - cram = "${test_data_dir}/genomics/homo_sapiens/scramble/test.cram" - cram_crai = "${test_data_dir}/genomics/homo_sapiens/scramble/test.cram.crai" - bed = "${test_data_dir}/genomics/homo_sapiens/scramble/test.bed" + fasta = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa" + fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai" + bam = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam" + bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai" + cram = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram" + cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai" + bed = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bed" + } + 'gene_set_analysis' { + gct = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct" + cls = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls" + gmx = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx" + } + 'cnvkit' { + amplicon_cnr = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr" + amplicon_cns = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns" } } 'bacteroides_fragilis' { 'genome' { - genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" - genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" - genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" - genome_gff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" + genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + genome_gbff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" + genome_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" + genome_gff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" } 'hamronization' { - genome_abricate_tsv = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" - genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" + genome_abricate_tsv = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" + genome_mapping_potential_arg = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" } 'illumina' { - test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" - test1_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" - test1_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" - test2_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" - test1_paired_end_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" - test1_paired_end_sorted_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam" - test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" - test2_paired_end_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" - test2_paired_end_sorted_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam" - test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" + test1_contigs_fa_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" + test1_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" + test1_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" + test1_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" + test1_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam" + test1_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" + test2_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" + test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" } 'nanopore' { - test_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz" - overlap_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf" + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz" + overlap_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf" } } 'candidatus_portiera_aleyrodidarum' { 'genome' { - genome_fasta = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta" - genome_sizes = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes" - genome_aln_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz" - genome_aln_nwk = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk" - proteome_fasta = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta" - test1_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff" - test2_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff" - test3_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff" + genome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta" + genome_sizes = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes" + genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz" + genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk" + proteome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta" + test1_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff" + test2_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff" + test3_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff" } 'illumina' { - test_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz" - test_se_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz" + test_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz" + test_se_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz" } 'nanopore' { - test_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz" + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz" } } 'haemophilus_influenzae' { 'genome' { - genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz" - genome_aln_gz = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz" - genome_aln_nwk = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk" + genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz" + genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz" + genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk" } } 'generic' { 'csv' { - test_csv = "${test_data_dir}/generic/csv/test.csv" + test_csv = "${params.test_data_base}/data/generic/csv/test.csv" } 'notebooks' { - rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" - ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md" - ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb" + rmarkdown = "${params.test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" + ipython_md = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md" + ipython_ipynb = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb" } 'tar' { - tar_gz = "${test_data_dir}/generic/tar/hello.tar.gz" + tar_gz = "${params.test_data_base}/data/generic/tar/hello.tar.gz" } 'tsv' { - test_tsv = "${test_data_dir}/generic/tsv/test.tsv" + test_tsv = "${params.test_data_base}/data/generic/tsv/test.tsv" } 'txt' { - hello = "${test_data_dir}/generic/txt/hello.txt" + hello = "${params.test_data_base}/data/generic/txt/hello.txt" } 'cooler'{ - test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" - test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" - test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" - test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" - test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" - hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" - test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" - test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" + test_pairix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" + test_pairix_pair_gz_px2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" + test_pairs_pair = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" + test_tabix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" + test_tabix_pair_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" + hg19_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" + test_merge_cool = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" + test_merge_cool_cp2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" } + 'pairtools' { + mock_4dedup_pairsam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4dedup.pairsam" + mock_4flip_pairs = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4flip.pairs" + mock_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.chrom.sizes" + mock_pairsam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.pairsam" + mock_sam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.sam" + frag_bed = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed" + } + 'estsfs'{ + config_file = "${params.test_data_base}/data/delete_me/estsfs/config-JC.txt" + data_file = "${params.test_data_base}/data/delete_me/estsfs/TEST-DATA.TXT" + seed_file = "${params.test_data_base}/data/delete_me/estsfs/seedfile.txt" + } 'config' { - ncbi_user_settings = "${test_data_dir}/generic/config/ncbi_user_settings.mkfg" + ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" + } + 'unsorted_data' { + 'unsorted_text' { + genome_file = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.genome" + intervals = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.bed" + numbers_csv = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.csv" + } } } - 'proteomics' { - 'msspectra' { - ups_file1 = "${test_data_dir}/proteomics/msspectra/OVEMB150205_12.raw" - ups_file2 = "${test_data_dir}/proteomics/msspectra/OVEMB150205_14.raw" - } - 'database' { - yeast_ups = "${test_data_dir}/proteomics/database/yeast_UPS.fasta" + 'proteomics' { + 'msspectra' { + ups_file1 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw" + ups_file2 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw" + profile_spectra = "${params.test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML" + } + 'database' { + yeast_ups = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta" + } + 'maxquant' { + mq_contrasts = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv" + mq_proteingroups = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_proteinGroups.txt" + mq_samplesheet = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_samplesheet.tsv" + mq_proteus_mat = "${params.test_data_base}/data/proteomics/maxquant/proteus.raw_MaxQuant_proteingroups_tab.tsv" + } + 'parameter' { + maxquant = "${params.test_data_base}/data/proteomics/parameter/mqpar.xml" + } + 'openms' { + idxml1 = "${params.test_data_base}/data/proteomics/openms/HepG2_rep1_small.idXML" + idxml2 = "${params.test_data_base}/data/proteomics/openms/HepG2_rep2_small.idXML" + } + 'pdb' { + tim1_pdb = "${params.test_data_base}/data/proteomics/pdb/1tim.pdb" + tim8_pdb = "${params.test_data_base}/data/proteomics/pdb/8tim.pdb" + } } - 'parameter' { - maxquant = "${test_data_dir}/proteomics/parameter/mqpar.xml" - } - } - 'mus_musculus' { - 'illumina' { - test_1_fastq_gz = "${test_data_dir}/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz" - test_2_fastq_gz = "${test_data_dir}/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz" + 'galaxea_fascicularis' { + hic { + pretext = "${params.test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext" + } } - 'csv' { - count_table = "${test_data_dir}/genomics/mus_musculus/mageck/count_table.csv" - library = "${test_data_dir}/genomics/mus_musculus/mageck/yusa_library.csv" + 'deilephila_porcellus' { + 'mito' { + ref_fa = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta" + ref_gb = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb" + hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa" + contigs = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa" } - 'txt' { - design_matrix = "${test_data_dir}/genomics/mus_musculus/mageck/design_matrix.txt" + } + 'imaging' { + 'h5' { + plant_wga = "${params.test_data_base}/data/imaging/h5/plant_wga.h5" + plant_wga_prob = "${params.test_data_base}/data/imaging/h5/plant_wga_probabilities.h5" } - - } + 'ilp' { + plant_wga_multicut = "${params.test_data_base}/data/imaging/ilp/plant_wga.multicut.ilp" + plant_wga_pixel_class = "${params.test_data_base}/data/imaging/ilp/plant_wga.pixel_prob.ilp" + } + 'tiff' { + mouse_heart_wga = "${params.test_data_base}/data/imaging/tiff/mindagap.mouse_heart.wga.tiff" + } + 'ome-tiff' { + cycif_tonsil_channels = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-channels.csv" + cycif_tonsil_cycle1 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycif_tonsil_cycle2 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + cycif_tonsil_cycle3 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif" + cycif_tonsil_dfp = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif" + cycif_tonsil_ffp = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif" + } + 'registration' { + markers = "${params.test_data_base}/data/imaging/registration/markers.csv" + cycle1 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycle2 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + } + 'segmentation' { + markers = "${params.test_data_base}/data/imaging/segmentation/markers.csv" + image = "${params.test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif" + } + 'quantification' { + markers = "${params.test_data_base}/data/imaging/quantification/markers.csv" + image = "${params.test_data_base}/data/imaging/quantification/cycif_tonsil_registered.ome.tif" + mask = "${params.test_data_base}/data/imaging/quantification/cell.ome.tif" + } + 'downstream' { + markers = "${params.test_data_base}/data/imaging/downstream/markers.csv" + cell_feature_array = "${params.test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv" + } + 'background_subtraction' { + markers = "${params.test_data_base}/data/imaging/background_subtraction/markers.csv" + image = "${params.test_data_base}/data/imaging/background_subtraction/cycif_tonsil_registered.ome.tif" + } + 'core_detection' { + image = "${params.test_data_base}/data/imaging/core_detection/single_core_dapi.tif" + } + } } } From 543a651405d66649bfafb460ddeae6d9b06e6c77 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 15:39:44 +0100 Subject: [PATCH 05/14] :white_check_mark: fix bcftools/concat tests --- tests/modules/nf-core/bcftools/concat/main.nf | 12 ++++++------ tests/modules/nf-core/bcftools/concat/test.yml | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/tests/modules/nf-core/bcftools/concat/main.nf b/tests/modules/nf-core/bcftools/concat/main.nf index 5ff032f..49960a9 100644 --- a/tests/modules/nf-core/bcftools/concat/main.nf +++ b/tests/modules/nf-core/bcftools/concat/main.nf @@ -7,10 +7,10 @@ include { BCFTOOLS_CONCAT } from '../../../../../modules/nf-core/bcftools/concat workflow test_bcftools_concat_tbi { input = [ [ id:'test3' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ] + [ file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) ] ] BCFTOOLS_CONCAT ( input ) @@ -19,8 +19,8 @@ workflow test_bcftools_concat_tbi { workflow test_bcftools_concat_no_tbi { input = [ [ id:'test3' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) ], [] ] diff --git a/tests/modules/nf-core/bcftools/concat/test.yml b/tests/modules/nf-core/bcftools/concat/test.yml index dd0fa4c..4ea393f 100644 --- a/tests/modules/nf-core/bcftools/concat/test.yml +++ b/tests/modules/nf-core/bcftools/concat/test.yml @@ -5,7 +5,7 @@ - bcftools/concat files: - path: output/bcftools/test3.vcf.gz - md5sum: 18c1612343f5e8a219ee6476a870a674 + md5sum: 4bcd0afd89f56c5d433f6b6abc44d0a6 - name: bcftools concat test_bcftools_concat_no_tbi command: nextflow run ./tests/modules/nf-core/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/concat/nextflow.config @@ -14,4 +14,4 @@ - bcftools/concat files: - path: output/bcftools/test3.vcf.gz - md5sum: 18c1612343f5e8a219ee6476a870a674 + md5sum: 4bcd0afd89f56c5d433f6b6abc44d0a6 From f8c8ed46e9a799006a98dd10ec2d68fc06d6a855 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 15:49:42 +0100 Subject: [PATCH 06/14] :wrench: prepend docker.io to custom docker images --- modules/cnr-ibba/freebayes/multi/main.nf | 2 +- modules/cnr-ibba/freebayes/splitbam/main.nf | 2 +- tests/modules/cnr-ibba/freebayes/chunk/test.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/cnr-ibba/freebayes/multi/main.nf b/modules/cnr-ibba/freebayes/multi/main.nf index 4906206..41c5550 100644 --- a/modules/cnr-ibba/freebayes/multi/main.nf +++ b/modules/cnr-ibba/freebayes/multi/main.nf @@ -4,7 +4,7 @@ process FREEBAYES_MULTI { label 'process_high' conda (params.enable_conda ? "bioconda::freebayes=1.3.6 main::numpy main::scipy" : null) - container "bunop/freebayes:v0.1" + container "docker.io/bunop/freebayes:v0.1" input: tuple val(meta), path(bam) diff --git a/modules/cnr-ibba/freebayes/splitbam/main.nf b/modules/cnr-ibba/freebayes/splitbam/main.nf index 1f4b8ab..4dff05c 100644 --- a/modules/cnr-ibba/freebayes/splitbam/main.nf +++ b/modules/cnr-ibba/freebayes/splitbam/main.nf @@ -4,7 +4,7 @@ process FREEBAYES_SPLITBAM { label 'process_single' conda (params.enable_conda ? "bioconda::freebayes=1.3.6 main::numpy main::scipy" : null) - container "bunop/freebayes:v0.1" + container "docker.io/bunop/freebayes:v0.1" input: tuple val(meta), path(bam) diff --git a/tests/modules/cnr-ibba/freebayes/chunk/test.yml b/tests/modules/cnr-ibba/freebayes/chunk/test.yml index 9555cbb..584656d 100644 --- a/tests/modules/cnr-ibba/freebayes/chunk/test.yml +++ b/tests/modules/cnr-ibba/freebayes/chunk/test.yml @@ -9,6 +9,6 @@ - path: output/freebayes/all.fb.regions.txt md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5 - path: output/freebayes/chr22:0-40001.vcf.gz - md5sum: 1a6cf708c4d737b2c32fee8198d01467 + md5sum: af568e83b7682a70988b9487f153f54a - path: output/freebayes/chr22:0-40001.vcf.gz.tbi md5sum: 83b1d5e5b36d61529d9d2d69cd4babc5 From 1a11b37d10839bacffd2da00046737184212aa42 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 17:25:03 +0100 Subject: [PATCH 07/14] :construction_worker: update lint workflow --- .github/workflows/nf-core-linting.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/nf-core-linting.yml b/.github/workflows/nf-core-linting.yml index b55a99b..b8420f4 100644 --- a/.github/workflows/nf-core-linting.yml +++ b/.github/workflows/nf-core-linting.yml @@ -54,9 +54,8 @@ jobs: - name: Install pip run: python -m pip install --upgrade pip - # Install a nf-core/tools custom release - name: Install nf-core tools development version - run: python -m pip install --upgrade --force-reinstall git+https://github.com/bunop/tools.git@custom-modules + run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev - name: Install Nextflow env: From e876593f055d08d74c70acc7d2ac0cc039809cee Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 17:49:04 +0100 Subject: [PATCH 08/14] :wrench: add schemas --- modules/environment-schema.json | 34 ++++++ modules/meta-schema.json | 186 ++++++++++++++++++++++++++++++++ modules/yaml-schema.json | 1 + 3 files changed, 221 insertions(+) create mode 100644 modules/environment-schema.json create mode 100644 modules/meta-schema.json create mode 120000 modules/yaml-schema.json diff --git a/modules/environment-schema.json b/modules/environment-schema.json new file mode 100644 index 0000000..ca7bdf6 --- /dev/null +++ b/modules/environment-schema.json @@ -0,0 +1,34 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "title": "conda environment yaml", + "description": "Validate the environment.yml file for an nf-core module", + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "The name of the component, same as in the meta.yml" + }, + "channels": { + "type": "array", + "items": [ + { + "enum": ["conda-forge"] + }, + { + "enum": ["bioconda"] + }, + { + "enum": ["defaults"] + } + ], + "minItems": 3 + }, + "dependencies": { + "type": "array", + "items": { + "type": "string" + } + } + }, + "required": ["name", "channels", "dependencies"] +} diff --git a/modules/meta-schema.json b/modules/meta-schema.json new file mode 100644 index 0000000..0b855d7 --- /dev/null +++ b/modules/meta-schema.json @@ -0,0 +1,186 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "title": "Meta yaml", + "description": "Validate the meta yaml file for an nf-core module", + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "Name of the module" + }, + "description": { + "type": "string", + "description": "Description of the module" + }, + "keywords": { + "type": "array", + "description": "Keywords for the module", + "items": { + "type": "string" + }, + "minItems": 3 + }, + "authors": { + "type": "array", + "description": "Authors of the module", + "items": { + "type": "string" + } + }, + "maintainers": { + "type": "array", + "description": "Maintainers of the module", + "items": { + "type": "string" + } + }, + "input": { + "type": "array", + "description": "Input channels for the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the input channel", + "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] + }, + "description": { + "type": "string", + "description": "Description of the input channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the input channel, given in Java glob syntax" + }, + "default": { + "type": ["string", "number", "boolean", "array", "object"], + "description": "Default value for the input channel" + }, + "enum": { + "type": "array", + "description": "List of allowed values for the input channel", + "items": { + "type": ["string", "number", "boolean", "array", "object"] + }, + "uniqueItems": true + } + }, + "required": ["type", "description"] + } + } + } + }, + "output": { + "type": "array", + "description": "Output channels for the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the output channel", + "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] + }, + "description": { + "type": "string", + "description": "Description of the output channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the input channel, given in Java glob syntax" + }, + "enum": { + "type": "array", + "description": "List of allowed values for the output channel", + "items": { + "type": ["string", "number", "boolean", "array", "object"] + }, + "uniqueItems": true + } + }, + "required": ["type", "description"] + } + } + } + }, + "tools": { + "type": "array", + "description": "Tools used by the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "description": { + "type": "string", + "description": "Description of the output channel" + }, + "homepage": { + "type": "string", + "description": "Homepage of the tool", + "pattern": "^(http|https)://.*$" + }, + "documentation": { + "type": "string", + "description": "Documentation of the tool", + "pattern": "^(http|https|ftp)://.*$" + }, + "tool_dev_url": { + "type": "string", + "description": "URL of the development version of the tool's documentation", + "pattern": "^(http|https)://.*$" + }, + "doi": { + "description": "DOI of the tool", + "anyOf": [ + { + "type": "string", + "pattern": "^10\\.\\d{4,9}\\/[^,]+$" + }, + { + "type": "string", + "enum": ["no DOI available"] + } + ] + }, + "licence": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Licence of the tool", + "minItems": 1, + "uniqueItems": true, + "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]" + } + }, + "required": ["description"], + "anyOf": [ + { + "required": ["homepage"] + }, + { + "required": ["documentation"] + }, + { + "required": ["tool_dev_url"] + }, + { + "required": ["doi"] + } + ] + } + } + } + } + }, + "required": ["name", "description", "keywords", "authors", "output", "tools"] +} diff --git a/modules/yaml-schema.json b/modules/yaml-schema.json new file mode 120000 index 0000000..d84030e --- /dev/null +++ b/modules/yaml-schema.json @@ -0,0 +1 @@ +meta-schema.json \ No newline at end of file From 0df6dad6fccf03d5bf452766dd1ea9795654338b Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 18:26:45 +0100 Subject: [PATCH 09/14] :rotating_light: attempt to solve lint issue --- modules/cnr-ibba/bamaddrg/environment.yml | 7 ++++ modules/cnr-ibba/bamaddrg/main.nf | 4 +-- modules/cnr-ibba/bamaddrg/meta.yml | 7 ++-- .../bamtools/coverage/environment.yml | 7 ++++ modules/cnr-ibba/bamtools/coverage/main.nf | 6 ++-- modules/cnr-ibba/bamtools/coverage/meta.yml | 13 ++++---- .../cnr-ibba/freebayes/chunk/environment.yml | 7 ++++ modules/cnr-ibba/freebayes/chunk/main.nf | 4 +-- modules/cnr-ibba/freebayes/chunk/meta.yml | 32 +++++++++++-------- .../cnr-ibba/freebayes/multi/environment.yml | 9 ++++++ modules/cnr-ibba/freebayes/multi/main.nf | 2 +- modules/cnr-ibba/freebayes/multi/meta.yml | 22 +++++++------ .../cnr-ibba/freebayes/single/environment.yml | 7 ++++ modules/cnr-ibba/freebayes/single/main.nf | 6 ++-- modules/cnr-ibba/freebayes/single/meta.yml | 26 ++++++++------- .../freebayes/splitbam/environment.yml | 9 ++++++ modules/cnr-ibba/freebayes/splitbam/main.nf | 2 +- modules/cnr-ibba/freebayes/splitbam/meta.yml | 20 ++++++------ modules/cnr-ibba/seqkit/rmdup/main.nf | 2 +- 19 files changed, 126 insertions(+), 66 deletions(-) create mode 100644 modules/cnr-ibba/bamaddrg/environment.yml create mode 100644 modules/cnr-ibba/bamtools/coverage/environment.yml create mode 100644 modules/cnr-ibba/freebayes/chunk/environment.yml create mode 100644 modules/cnr-ibba/freebayes/multi/environment.yml create mode 100644 modules/cnr-ibba/freebayes/single/environment.yml create mode 100644 modules/cnr-ibba/freebayes/splitbam/environment.yml diff --git a/modules/cnr-ibba/bamaddrg/environment.yml b/modules/cnr-ibba/bamaddrg/environment.yml new file mode 100644 index 0000000..b48438a --- /dev/null +++ b/modules/cnr-ibba/bamaddrg/environment.yml @@ -0,0 +1,7 @@ +name: bamaddrg +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bamaddrg=9baba65f88228e55639689a3cea38dd150e6284f diff --git a/modules/cnr-ibba/bamaddrg/main.nf b/modules/cnr-ibba/bamaddrg/main.nf index 5d04968..98fb0ca 100644 --- a/modules/cnr-ibba/bamaddrg/main.nf +++ b/modules/cnr-ibba/bamaddrg/main.nf @@ -3,10 +3,10 @@ process BAMADDRG { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::bamaddrg=9baba65f88228e55639689a3cea38dd150e6284f" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1': - 'quay.io/biocontainers/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1' }" + 'biocontainers/bamaddrg:9baba65f88228e55639689a3cea38dd150e6284f--ha89c123_1' }" input: tuple val(meta), path(bam) diff --git a/modules/cnr-ibba/bamaddrg/meta.yml b/modules/cnr-ibba/bamaddrg/meta.yml index 453dea1..2b9c1bb 100644 --- a/modules/cnr-ibba/bamaddrg/meta.yml +++ b/modules/cnr-ibba/bamaddrg/meta.yml @@ -2,14 +2,17 @@ name: "bamaddrg" description: adds read groups to input BAM files keywords: - sort + - add + - read + - group + - bam tools: - "bamaddrg": description: "Add read group to BAM files" homepage: "https://github.com/ekg/bamaddrg" documentation: "https://github.com/ekg/bamaddrg" tool_dev_url: "https://github.com/ekg/bamaddrg" - doi: "" - licence: "['MIT']" + licence: ["MIT"] input: # Only when we have meta diff --git a/modules/cnr-ibba/bamtools/coverage/environment.yml b/modules/cnr-ibba/bamtools/coverage/environment.yml new file mode 100644 index 0000000..31cc51d --- /dev/null +++ b/modules/cnr-ibba/bamtools/coverage/environment.yml @@ -0,0 +1,7 @@ +name: bamtools_coverage +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bamtools=2.5.2 diff --git a/modules/cnr-ibba/bamtools/coverage/main.nf b/modules/cnr-ibba/bamtools/coverage/main.nf index 35a9f6d..ec1206a 100644 --- a/modules/cnr-ibba/bamtools/coverage/main.nf +++ b/modules/cnr-ibba/bamtools/coverage/main.nf @@ -3,10 +3,10 @@ process BAMTOOLS_COVERAGE { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0': - 'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }" + 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hdcf5f25_2' : + 'biocontainers/bamtools:2.5.2--hdcf5f25_2' }" input: tuple val(meta), path(bam) diff --git a/modules/cnr-ibba/bamtools/coverage/meta.yml b/modules/cnr-ibba/bamtools/coverage/meta.yml index a2b22f2..ecd0981 100644 --- a/modules/cnr-ibba/bamtools/coverage/meta.yml +++ b/modules/cnr-ibba/bamtools/coverage/meta.yml @@ -6,13 +6,12 @@ keywords: - bam - coverage tools: - - "bamtools": - description: "C++ API & command-line toolkit for working with BAM data" - homepage: "http://github.com/pezmaster31/bamtools" - documentation: "https://github.com/pezmaster31/bamtools/wiki" - tool_dev_url: "http://github.com/pezmaster31/bamtools" - doi: "" - licence: "['MIT']" + - bamtools: + description: C++ API & command-line toolkit for working with BAM data + homepage: http://github.com/pezmaster31/bamtools + documentation: https://github.com/pezmaster31/bamtools/wiki + tool_dev_url: http://github.com/pezmaster31/bamtools + licence: ["MIT"] input: - meta: diff --git a/modules/cnr-ibba/freebayes/chunk/environment.yml b/modules/cnr-ibba/freebayes/chunk/environment.yml new file mode 100644 index 0000000..6846080 --- /dev/null +++ b/modules/cnr-ibba/freebayes/chunk/environment.yml @@ -0,0 +1,7 @@ +name: freebayes +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::freebayes=1.3.6 diff --git a/modules/cnr-ibba/freebayes/chunk/main.nf b/modules/cnr-ibba/freebayes/chunk/main.nf index b596191..f6aafff 100644 --- a/modules/cnr-ibba/freebayes/chunk/main.nf +++ b/modules/cnr-ibba/freebayes/chunk/main.nf @@ -4,10 +4,10 @@ process FREEBAYES_CHUNK { label 'process_low' label 'error_retry' - conda (params.enable_conda ? "bioconda::freebayes=1.3.6" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0': - 'quay.io/biocontainers/freebayes:1.3.6--hb089aa1_0' }" + 'biocontainers/freebayes:1.3.6--hb089aa1_0' }" input: tuple val(meta), val(region) diff --git a/modules/cnr-ibba/freebayes/chunk/meta.yml b/modules/cnr-ibba/freebayes/chunk/meta.yml index c60b409..7c35f24 100644 --- a/modules/cnr-ibba/freebayes/chunk/meta.yml +++ b/modules/cnr-ibba/freebayes/chunk/meta.yml @@ -1,16 +1,20 @@ name: "freebayes_chunk" -description: Run freebayes on sample +description: Run freebayes on a sample chunk keywords: - freebayes - - single + - chunk + - variant caller + - SNP + - genotyping + - bayesian tools: - - "freebayes": - description: "Bayesian haplotype-based polymorphism discovery and genotyping" - homepage: "https://github.com/freebayes/freebayes" - documentation: "None" - tool_dev_url: "None" - doi: "" - licence: "['MIT']" + - freebayes: + description: Bayesian haplotype-based polymorphism discovery and genotyping + homepage: https://github.com/freebayes/freebayes + documentation: https://github.com/freebayes/freebayes + tool_dev_url: https://github.com/freebayes/freebayes + doi: "10.48550/arXiv.1207.3907" + license: ["MIT"] input: - meta: @@ -19,10 +23,10 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - region: - type: value + type: string description: A region in which genotypes will be called (chrom:start-end) - bam: - type: path + type: file description: a BAM file pattern: "*.{bam}" - bai: @@ -30,7 +34,7 @@ input: description: Index for BAM file pattern: "*.{bai}" - bam_list: - type: path + type: file description: A txt file in which all bam file names are described pattern: "*.list.txt" - genome_fasta: @@ -49,11 +53,11 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: - type: path + type: file description: VCF compressed with bgzip pattern: "*.{vcf.gz}" - index: - type: path + type: file description: VCF indexed with tabix pattern: "*.{vcf.gz.tbi}" - version: diff --git a/modules/cnr-ibba/freebayes/multi/environment.yml b/modules/cnr-ibba/freebayes/multi/environment.yml new file mode 100644 index 0000000..fd24254 --- /dev/null +++ b/modules/cnr-ibba/freebayes/multi/environment.yml @@ -0,0 +1,9 @@ +name: freebayes +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::freebayes=1.3.6 + - main::numpy + - main::scipy diff --git a/modules/cnr-ibba/freebayes/multi/main.nf b/modules/cnr-ibba/freebayes/multi/main.nf index 41c5550..114bebf 100644 --- a/modules/cnr-ibba/freebayes/multi/main.nf +++ b/modules/cnr-ibba/freebayes/multi/main.nf @@ -3,7 +3,7 @@ process FREEBAYES_MULTI { tag "freebayes.multi" label 'process_high' - conda (params.enable_conda ? "bioconda::freebayes=1.3.6 main::numpy main::scipy" : null) + conda "${moduleDir}/environment.yml" container "docker.io/bunop/freebayes:v0.1" input: diff --git a/modules/cnr-ibba/freebayes/multi/meta.yml b/modules/cnr-ibba/freebayes/multi/meta.yml index e47f73d..aaa6f36 100644 --- a/modules/cnr-ibba/freebayes/multi/meta.yml +++ b/modules/cnr-ibba/freebayes/multi/meta.yml @@ -3,14 +3,18 @@ description: Run freebayes on multiple BAM files keywords: - freebayes - multi + - variant caller + - SNP + - genotyping + - bayesian tools: - freebayes: description: Bayesian haplotype-based polymorphism discovery and genotyping homepage: https://github.com/freebayes/freebayes - documentation: None - tool_dev_url: None - doi: "" - licence: ["MIT"] + documentation: https://github.com/freebayes/freebayes + tool_dev_url: https://github.com/freebayes/freebayes + doi: "10.48550/arXiv.1207.3907" + license: ["MIT"] input: - meta: @@ -19,15 +23,15 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: - type: path + type: file description: A list of BAM files pattern: "*.{bam}" - bai: - type: path + type: file description: A list of BAM index files pattern: "*.{bai}" - genome_fasta: - type: path + type: file description: The genome fasta file (not compressed) pattern: "*.{fa,fasta}" - genome_fasta_fai: @@ -42,11 +46,11 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: - type: path + type: file description: | VCF compressed with bgzip (always all.fb.vcf.gz) - index: - type: path + type: file description: | VCF indexed with tabix (always all.fb.vcf.gz.tbi) - version: diff --git a/modules/cnr-ibba/freebayes/single/environment.yml b/modules/cnr-ibba/freebayes/single/environment.yml new file mode 100644 index 0000000..6846080 --- /dev/null +++ b/modules/cnr-ibba/freebayes/single/environment.yml @@ -0,0 +1,7 @@ +name: freebayes +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::freebayes=1.3.6 diff --git a/modules/cnr-ibba/freebayes/single/main.nf b/modules/cnr-ibba/freebayes/single/main.nf index b1a3875..e1ea7c1 100644 --- a/modules/cnr-ibba/freebayes/single/main.nf +++ b/modules/cnr-ibba/freebayes/single/main.nf @@ -3,10 +3,10 @@ process FREEBAYES_SINGLE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::freebayes=1.3.6" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0' : - 'quay.io/biocontainers/freebayes:1.3.6--hb089aa1_0' }" + 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0': + 'biocontainers/freebayes:1.3.6--hb089aa1_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/cnr-ibba/freebayes/single/meta.yml b/modules/cnr-ibba/freebayes/single/meta.yml index 2b74ae9..e9414d3 100644 --- a/modules/cnr-ibba/freebayes/single/meta.yml +++ b/modules/cnr-ibba/freebayes/single/meta.yml @@ -3,14 +3,18 @@ description: Run freebayes on sample keywords: - freebayes - single + - variant caller + - SNP + - genotyping + - bayesian tools: - - "freebayes": - description: "Bayesian haplotype-based polymorphism discovery and genotyping" - homepage: "https://github.com/freebayes/freebayes" - documentation: "None" - tool_dev_url: "None" - doi: "" - licence: "['MIT']" + - freebayes: + description: Bayesian haplotype-based polymorphism discovery and genotyping + homepage: https://github.com/freebayes/freebayes + documentation: https://github.com/freebayes/freebayes + tool_dev_url: https://github.com/freebayes/freebayes + doi: "10.48550/arXiv.1207.3907" + license: ["MIT"] input: - meta: @@ -19,7 +23,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: - type: path + type: file description: a BAM file pattern: "*.{bam}" - bai: @@ -35,7 +39,7 @@ input: description: reference fasta file index pattern: "*.{fa,fasta}.fai" - num_regions: - type: optional value + type: integer description: Number of regions to split freebayes input (default $task.cpus) output: @@ -45,11 +49,11 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: - type: path + type: file description: VCF compressed with bgzip pattern: "*.{vcf.gz}" - index: - type: path + type: file description: VCF indexed with tabix pattern: "*.{vcf.gz.tbi}" - version: diff --git a/modules/cnr-ibba/freebayes/splitbam/environment.yml b/modules/cnr-ibba/freebayes/splitbam/environment.yml new file mode 100644 index 0000000..fd24254 --- /dev/null +++ b/modules/cnr-ibba/freebayes/splitbam/environment.yml @@ -0,0 +1,9 @@ +name: freebayes +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::freebayes=1.3.6 + - main::numpy + - main::scipy diff --git a/modules/cnr-ibba/freebayes/splitbam/main.nf b/modules/cnr-ibba/freebayes/splitbam/main.nf index 4dff05c..5903444 100644 --- a/modules/cnr-ibba/freebayes/splitbam/main.nf +++ b/modules/cnr-ibba/freebayes/splitbam/main.nf @@ -3,7 +3,7 @@ process FREEBAYES_SPLITBAM { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::freebayes=1.3.6 main::numpy main::scipy" : null) + conda "${moduleDir}/environment.yml" container "docker.io/bunop/freebayes:v0.1" input: diff --git a/modules/cnr-ibba/freebayes/splitbam/meta.yml b/modules/cnr-ibba/freebayes/splitbam/meta.yml index 3b8de86..ec41b7e 100644 --- a/modules/cnr-ibba/freebayes/splitbam/meta.yml +++ b/modules/cnr-ibba/freebayes/splitbam/meta.yml @@ -5,13 +5,13 @@ keywords: - splitbam - split_ref_by_bai_datasize tools: - - "freebayes": - description: "Bayesian haplotype-based polymorphism discovery and genotyping" - homepage: "https://github.com/freebayes/freebayes" - documentation: "None" - tool_dev_url: "None" - doi: "" - licence: "['MIT']" + - freebayes: + description: Bayesian haplotype-based polymorphism discovery and genotyping + homepage: https://github.com/freebayes/freebayes + documentation: https://github.com/freebayes/freebayes + tool_dev_url: https://github.com/freebayes/freebayes + doi: "10.48550/arXiv.1207.3907" + license: ["MIT"] input: - meta: @@ -20,15 +20,15 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: - type: path + type: file description: A list of BAM files pattern: "*.{bam}" - bai: - type: path + type: file description: A list of BAM index files pattern: "*.{bai}" - genome_fasta: - type: path + type: file description: The genome fasta file (not compressed) pattern: "*.{fa,fasta}" - genome_fasta_fai: diff --git a/modules/cnr-ibba/seqkit/rmdup/main.nf b/modules/cnr-ibba/seqkit/rmdup/main.nf index dc28744..6408fc1 100644 --- a/modules/cnr-ibba/seqkit/rmdup/main.nf +++ b/modules/cnr-ibba/seqkit/rmdup/main.nf @@ -5,7 +5,7 @@ process SEQKIT_RMDUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqkit:2.6.0--h9ee0642_0': - 'quay.io/biocontainers/seqkit:2.6.0--h9ee0642_0' }" + 'biocontainers/seqkit:2.6.0--h9ee0642_0' }" input: tuple val(meta), path(sequence) From 9628bce6557b64669ac50b9c3d6e090c4cd6d0bb Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 18:59:31 +0100 Subject: [PATCH 10/14] :rotating_light: solve issues with linting --- modules/cnr-ibba/freebayes/chunk/environment.yml | 2 +- modules/cnr-ibba/freebayes/multi/environment.yml | 2 +- modules/cnr-ibba/freebayes/single/environment.yml | 2 +- modules/cnr-ibba/freebayes/splitbam/environment.yml | 2 +- modules/cnr-ibba/seqkit/rmdup/environment.yml | 1 + 5 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/cnr-ibba/freebayes/chunk/environment.yml b/modules/cnr-ibba/freebayes/chunk/environment.yml index 6846080..f583435 100644 --- a/modules/cnr-ibba/freebayes/chunk/environment.yml +++ b/modules/cnr-ibba/freebayes/chunk/environment.yml @@ -1,4 +1,4 @@ -name: freebayes +name: freebayes_chunk channels: - conda-forge - bioconda diff --git a/modules/cnr-ibba/freebayes/multi/environment.yml b/modules/cnr-ibba/freebayes/multi/environment.yml index fd24254..bb8e562 100644 --- a/modules/cnr-ibba/freebayes/multi/environment.yml +++ b/modules/cnr-ibba/freebayes/multi/environment.yml @@ -1,4 +1,4 @@ -name: freebayes +name: freebayes_multi channels: - conda-forge - bioconda diff --git a/modules/cnr-ibba/freebayes/single/environment.yml b/modules/cnr-ibba/freebayes/single/environment.yml index 6846080..4c99799 100644 --- a/modules/cnr-ibba/freebayes/single/environment.yml +++ b/modules/cnr-ibba/freebayes/single/environment.yml @@ -1,4 +1,4 @@ -name: freebayes +name: freebayes_single channels: - conda-forge - bioconda diff --git a/modules/cnr-ibba/freebayes/splitbam/environment.yml b/modules/cnr-ibba/freebayes/splitbam/environment.yml index fd24254..b2ff92c 100644 --- a/modules/cnr-ibba/freebayes/splitbam/environment.yml +++ b/modules/cnr-ibba/freebayes/splitbam/environment.yml @@ -1,4 +1,4 @@ -name: freebayes +name: freebayes_splitbam channels: - conda-forge - bioconda diff --git a/modules/cnr-ibba/seqkit/rmdup/environment.yml b/modules/cnr-ibba/seqkit/rmdup/environment.yml index 7d4c06b..15cf89a 100644 --- a/modules/cnr-ibba/seqkit/rmdup/environment.yml +++ b/modules/cnr-ibba/seqkit/rmdup/environment.yml @@ -1,3 +1,4 @@ +name: seqkit_rmdup channels: - conda-forge - bioconda From abc517f0113fa941f2f9d02758b0206739651e4f Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 18:59:42 +0100 Subject: [PATCH 11/14] :rotating_light: minor changes in metas --- modules/cnr-ibba/freebayes/chunk/meta.yml | 7 ++++++- modules/cnr-ibba/freebayes/multi/meta.yml | 2 +- modules/cnr-ibba/freebayes/single/meta.yml | 6 +++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/modules/cnr-ibba/freebayes/chunk/meta.yml b/modules/cnr-ibba/freebayes/chunk/meta.yml index 7c35f24..7601ff8 100644 --- a/modules/cnr-ibba/freebayes/chunk/meta.yml +++ b/modules/cnr-ibba/freebayes/chunk/meta.yml @@ -18,6 +18,11 @@ tools: input: - meta: + type: map + description: | + Groovy Map containing information on a region + e.g. [ id:'test', single_end:false ] + - sample_meta: type: map description: | Groovy Map containing sample information @@ -60,7 +65,7 @@ output: type: file description: VCF indexed with tabix pattern: "*.{vcf.gz.tbi}" - - version: + - versions: type: file description: File containing software version pattern: "*.{version.txt}" diff --git a/modules/cnr-ibba/freebayes/multi/meta.yml b/modules/cnr-ibba/freebayes/multi/meta.yml index aaa6f36..5947849 100644 --- a/modules/cnr-ibba/freebayes/multi/meta.yml +++ b/modules/cnr-ibba/freebayes/multi/meta.yml @@ -53,7 +53,7 @@ output: type: file description: | VCF indexed with tabix (always all.fb.vcf.gz.tbi) - - version: + - versions: type: file description: File containing software version pattern: "*.{version.txt}" diff --git a/modules/cnr-ibba/freebayes/single/meta.yml b/modules/cnr-ibba/freebayes/single/meta.yml index e9414d3..2dbbc95 100644 --- a/modules/cnr-ibba/freebayes/single/meta.yml +++ b/modules/cnr-ibba/freebayes/single/meta.yml @@ -30,6 +30,10 @@ input: type: file description: Index for BAM file pattern: "*.{bai}" + - coverage: + type: file + description: Bamtools coverage output + pattern: "*.{txt}" - genome_fasta: type: file description: The genome fasta file (not compressed) @@ -56,7 +60,7 @@ output: type: file description: VCF indexed with tabix pattern: "*.{vcf.gz.tbi}" - - version: + - versions: type: file description: File containing software version pattern: "*.{version.txt}" From 3999a1514ba0d61793580008b1086750ed915748 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Dec 2023 21:08:48 +0100 Subject: [PATCH 12/14] :white_check_mark: attempt to solve some issues --- modules/nf-core/bcftools/concat/environment.yml | 7 +++++++ modules/nf-core/bcftools/concat/main.nf | 17 ++++++++++++++--- modules/nf-core/bcftools/concat/meta.yml | 9 ++++++--- modules/nf-core/tabix/tabix/environment.yml | 7 +++++++ modules/nf-core/tabix/tabix/main.nf | 4 ++-- modules/nf-core/tabix/tabix/meta.yml | 4 ++++ .../cnr-ibba/freebayes/splitbam/test.yml | 1 - .../cnr-ibba/freebayes_parallel/test.yml | 1 - 8 files changed, 40 insertions(+), 10 deletions(-) create mode 100644 modules/nf-core/bcftools/concat/environment.yml create mode 100644 modules/nf-core/tabix/tabix/environment.yml diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml new file mode 100644 index 0000000..ff0200d --- /dev/null +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -0,0 +1,7 @@ +name: bcftools_concat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.18 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 89078f7..a5830a2 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bcftools=1.16" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': + 'biocontainers/bcftools:1.18--h8b25389_0' }" input: tuple val(meta), path(vcfs), path(tbi) @@ -32,4 +32,15 @@ process BCFTOOLS_CONCAT { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index 167dbe5..91cb54d 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -5,7 +5,6 @@ keywords: - concat - bcftools - VCF - tools: - concat: description: | @@ -21,12 +20,12 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcfs: - type: files + type: list description: | List containing 2 or more vcf files e.g. [ 'file1.vcf', 'file2.vcf' ] - tbi: - type: files + type: list description: | List containing 2 or more index files (optional) e.g. [ 'file1.tbi', 'file2.tbi' ] @@ -46,3 +45,7 @@ output: pattern: "versions.yml" authors: - "@abhi18av" + - "@nvnieuwk" +maintainers: + - "@abhi18av" + - "@nvnieuwk" diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml new file mode 100644 index 0000000..7167fb8 --- /dev/null +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -0,0 +1,7 @@ +name: tabix_tabix +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 21b2e79..c304a8a 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -2,10 +2,10 @@ process TABIX_TABIX { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? 'bioconda::tabix=1.11' : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + 'biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index fcc6e52..ae5b4f4 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -43,3 +43,7 @@ authors: - "@joseespinosa" - "@drpatelh" - "@maxulysse" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/tests/modules/cnr-ibba/freebayes/splitbam/test.yml b/tests/modules/cnr-ibba/freebayes/splitbam/test.yml index 662dff3..0bbc945 100644 --- a/tests/modules/cnr-ibba/freebayes/splitbam/test.yml +++ b/tests/modules/cnr-ibba/freebayes/splitbam/test.yml @@ -5,6 +5,5 @@ - freebayes/splitbam files: - path: output/freebayes/all.fb.list.txt - md5sum: 4f35504d05254179c9c0472ad0d96692 - path: output/freebayes/all.fb.regions.txt md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5 diff --git a/tests/subworkflows/cnr-ibba/freebayes_parallel/test.yml b/tests/subworkflows/cnr-ibba/freebayes_parallel/test.yml index 99e59fa..c9e98bb 100644 --- a/tests/subworkflows/cnr-ibba/freebayes_parallel/test.yml +++ b/tests/subworkflows/cnr-ibba/freebayes_parallel/test.yml @@ -8,7 +8,6 @@ - subworkflows/freebayes_parallel files: - path: output/freebayes/all.fb.list.txt - md5sum: 4f35504d05254179c9c0472ad0d96692 - path: output/freebayes/all.fb.regions.txt md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5 - path: output/freebayes/all-samples.vcf.gz From c9fc97ae66cbb4d0bc21e66e62ecc2fee0734cc3 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 18 Dec 2023 15:50:31 +0100 Subject: [PATCH 13/14] :arrow_up: updare nf-core modules --- .../nf-core/samtools/coverage/environment.yml | 7 + modules/nf-core/samtools/coverage/main.nf | 42 +++--- modules/nf-core/samtools/coverage/meta.yml | 28 ++-- .../nf-core/samtools/flagstat/environment.yml | 7 + modules/nf-core/samtools/flagstat/main.nf | 21 ++- modules/nf-core/samtools/flagstat/meta.yml | 4 +- .../nf-core/samtools/idxstats/environment.yml | 7 + modules/nf-core/samtools/idxstats/main.nf | 21 ++- modules/nf-core/samtools/idxstats/meta.yml | 4 +- .../samtools/idxstats/tests/main.nf.test | 36 +++++ .../samtools/idxstats/tests/main.nf.test.snap | 16 +++ .../nf-core/samtools/idxstats/tests/tags.yml | 2 + .../nf-core/samtools/stats/environment.yml | 7 + modules/nf-core/samtools/stats/main.nf | 12 +- modules/nf-core/samtools/stats/meta.yml | 28 ++-- .../nf-core/bam_stats_samtools/main.nf | 18 +-- .../nf-core/bam_stats_samtools/meta.yml | 57 ++++---- .../bam_stats_samtools/tests/main.nf.test | 102 ++++++++++++++ .../tests/main.nf.test.snap | 128 ++++++++++++++++++ .../nf-core/bam_stats_samtools/tests/tags.yml | 2 + .../modules/nf-core/samtools/coverage/main.nf | 9 +- .../nf-core/samtools/coverage/test.yml | 7 +- tests/modules/nf-core/samtools/stats/main.nf | 9 +- tests/modules/nf-core/samtools/stats/test.yml | 4 +- .../nf-core/bam_stats_samtools/main.nf | 15 +- .../nf-core/bam_stats_samtools/test.yml | 6 +- 26 files changed, 476 insertions(+), 123 deletions(-) create mode 100644 modules/nf-core/samtools/coverage/environment.yml create mode 100644 modules/nf-core/samtools/flagstat/environment.yml create mode 100644 modules/nf-core/samtools/idxstats/environment.yml create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/idxstats/tests/tags.yml create mode 100644 modules/nf-core/samtools/stats/environment.yml create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/tags.yml diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml new file mode 100644 index 0000000..6f13872 --- /dev/null +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -0,0 +1,7 @@ +name: samtools_coverage +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf index c44b8dd..226cbb1 100644 --- a/modules/nf-core/samtools/coverage/main.nf +++ b/modules/nf-core/samtools/coverage/main.nf @@ -1,45 +1,47 @@ - process SAMTOOLS_COVERAGE { tag "$meta.id" - label 'process_low' + label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: - tuple val(meta), path(bam) + tuple val(meta), path(input), path(input_index) output: - tuple val(meta), path("*.{csv,txt}"), emit: report - path "versions.yml" , emit: versions + tuple val(meta), path("*.txt"), emit: coverage + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: "" + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ samtools \\ coverage \\ $args \\ - --output ${prefix}.csv \\ - $bam + -o ${prefix}.txt \\ + $input - samtools \\ - coverage \\ - $args2 \\ - --histogram \\ - --ascii \\ - --output ${prefix}.txt \\ - $bam + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )) + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ) END_VERSIONS """ } diff --git a/modules/nf-core/samtools/coverage/meta.yml b/modules/nf-core/samtools/coverage/meta.yml index d4377b3..4b57609 100644 --- a/modules/nf-core/samtools/coverage/meta.yml +++ b/modules/nf-core/samtools/coverage/meta.yml @@ -1,10 +1,9 @@ name: "samtools_coverage" description: produces a histogram or table of coverage per chromosome keywords: - - coverage + - depth + - samtools - bam - - sam - - cram tools: - samtools: description: | @@ -12,35 +11,38 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] - input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bam: + - input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - report: - type: file - description: File containing samtools coverage output - pattern: "*.{csv,txt}" - versions: type: file description: File containing software versions pattern: "versions.yml" - + - coverage: + type: file + description: Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram). + pattern: "*.txt" authors: - - "@bunop" + - "@LouisLeNezet" +maintainers: + - "@LouisLeNezet" diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml new file mode 100644 index 0000000..5efae05 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -0,0 +1,7 @@ +name: samtools_flagstat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 40b283e..f1893d7 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -1,11 +1,11 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" - label 'process_low' + label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam), path(bai) @@ -23,7 +23,7 @@ process SAMTOOLS_FLAGSTAT { """ samtools \\ flagstat \\ - --threads ${task.cpus-1} \\ + --threads ${task.cpus} \\ $bam \\ > ${prefix}.flagstat @@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.flagstat + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 9526906..9799135 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -14,7 +14,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: @@ -47,3 +47,5 @@ output: pattern: "versions.yml" authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml new file mode 100644 index 0000000..2401db0 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -0,0 +1,7 @@ +name: samtools_idxstats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index bd2582c..00d916b 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -1,11 +1,11 @@ process SAMTOOLS_IDXSTATS { tag "$meta.id" - label 'process_low' + label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam), path(bai) @@ -24,6 +24,7 @@ process SAMTOOLS_IDXSTATS { """ samtools \\ idxstats \\ + --threads ${task.cpus-1} \\ $bam \\ > ${prefix}.idxstats @@ -32,4 +33,16 @@ process SAMTOOLS_IDXSTATS { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.idxstats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 3710ab8..344e92a 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -15,7 +15,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: @@ -48,3 +48,5 @@ output: pattern: "versions.yml" authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test new file mode 100644 index 0000000..f6c9215 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_IDXSTATS" + script "../main.nf" + process "SAMTOOLS_IDXSTATS" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/idxstats" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.idxstats).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap new file mode 100644 index 0000000..4c6c12b --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "timestamp": "2023-11-14T15:52:19.875194" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml new file mode 100644 index 0000000..d3057c6 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/idxstats: + - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml new file mode 100644 index 0000000..b89ce64 --- /dev/null +++ b/modules/nf-core/samtools/stats/environment.yml @@ -0,0 +1,7 @@ +name: samtools_stats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index fd91ac2..7539140 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -1,15 +1,15 @@ process SAMTOOLS_STATS { tag "$meta.id" - label 'process_low' + label 'process_single' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input), path(input_index) - path fasta + tuple val(meta2), path(fasta) output: tuple val(meta), path("*.stats"), emit: stats @@ -25,7 +25,7 @@ process SAMTOOLS_STATS { """ samtools \\ stats \\ - --threads ${task.cpus-1} \\ + --threads ${task.cpus} \\ ${reference} \\ ${input} \\ > ${prefix}.stats diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index cac50b1..735ff81 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -13,7 +13,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: @@ -23,16 +23,21 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: - type: optional file - description: Reference file the CRAM was created with + type: file + description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" output: - meta: @@ -51,3 +56,8 @@ output: authors: - "@drpatelh" - "@FriederikeHanssen" + - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf index cfcc48d..44d4c01 100644 --- a/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -8,25 +8,25 @@ include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/m workflow BAM_STATS_SAMTOOLS { take: - bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ] - fasta // channel: [ fasta ] + ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + ch_fasta // channel: [ val(meta), path(fasta) ] main: ch_versions = Channel.empty() - SAMTOOLS_STATS ( bam_bai, fasta ) + SAMTOOLS_STATS ( ch_bam_bai, ch_fasta ) ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) - SAMTOOLS_FLAGSTAT ( bam_bai ) + SAMTOOLS_FLAGSTAT ( ch_bam_bai ) ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) - SAMTOOLS_IDXSTATS ( bam_bai ) + SAMTOOLS_IDXSTATS ( ch_bam_bai ) ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions) emit: - stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] + flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ] - versions = ch_versions // channel: [ versions.yml ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml index 5252b0e..809bf73 100644 --- a/subworkflows/nf-core/bam_stats_samtools/meta.yml +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json name: bam_stats_samtools description: Produces comprehensive statistics from SAM/BAM/CRAM file keywords: @@ -6,49 +7,37 @@ keywords: - bam - sam - cram -modules: +components: - samtools/stats - samtools/idxstats - samtools/flagstat input: - - meta: - type: map + - ch_bam_bai: description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" -output: - - meta: - type: map + The input channel containing the BAM/CRAM and it's index + Structure: [ val(meta), path(bam), path(bai) ] + - ch_fasta: description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Reference genome fasta file + Structure: [ path(fasta) ] +output: - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats)] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Files containing software versions + Structure: [ path(versions.yml) ] authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test new file mode 100644 index 0000000..9721089 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -0,0 +1,102 @@ +nextflow_workflow { + + name "Test Workflow BAM_STATS_SAMTOOLS" + script "../main.nf" + workflow "BAM_STATS_SAMTOOLS" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "bam_stats_samtools" + tag "subworkflows/bam_stats_samtools" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/stats" + + test("test_bam_stats_samtools_single_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_single_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end_cram") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_cram_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_cram_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_cram_idxstats") } + ) + } + } + +} diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap new file mode 100644 index 0000000..d3af137 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -0,0 +1,128 @@ +{ + "test_bam_stats_samtools_paired_end_cram_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781" + ] + ] + ], + "timestamp": "2023-11-06T09:31:26.194017574" + }, + "test_bam_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,49e2b43344ff92bc4c02463a58f7ba4a" + ] + ] + ], + "timestamp": "2023-12-04T11:07:13.965061942" + }, + "test_bam_stats_samtools_paired_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "timestamp": "2023-11-06T09:31:11.668517251" + }, + "test_bam_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "timestamp": "2023-11-06T09:26:10.340046381" + }, + "test_bam_stats_samtools_paired_end_cram_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15" + ] + ] + ], + "timestamp": "2023-11-06T09:31:26.207052003" + }, + "test_bam_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,5a6667d97806e5002731e9cf23674fad" + ] + ] + ], + "timestamp": "2023-12-04T11:07:06.676820877" + }, + "test_bam_stats_samtools_paired_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "timestamp": "2023-11-06T09:31:11.68246157" + }, + "test_bam_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "timestamp": "2023-11-06T09:26:10.349439801" + }, + "test_bam_stats_samtools_paired_end_cram_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,2cf2fe93596ee3d74f946097b204a629" + ] + ] + ], + "timestamp": "2023-12-04T11:07:22.30295557" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml new file mode 100644 index 0000000..ec2f2d6 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_stats_samtools: + - subworkflows/nf-core/bam_stats_samtools/** diff --git a/tests/modules/nf-core/samtools/coverage/main.nf b/tests/modules/nf-core/samtools/coverage/main.nf index 4617944..a4a7ce4 100644 --- a/tests/modules/nf-core/samtools/coverage/main.nf +++ b/tests/modules/nf-core/samtools/coverage/main.nf @@ -5,11 +5,8 @@ nextflow.enable.dsl = 2 include { SAMTOOLS_COVERAGE } from '../../../../../modules/nf-core/samtools/coverage/main.nf' workflow test_samtools_coverage { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)] SAMTOOLS_COVERAGE ( input ) } diff --git a/tests/modules/nf-core/samtools/coverage/test.yml b/tests/modules/nf-core/samtools/coverage/test.yml index 5e62fe9..9e57de9 100644 --- a/tests/modules/nf-core/samtools/coverage/test.yml +++ b/tests/modules/nf-core/samtools/coverage/test.yml @@ -1,10 +1,9 @@ - name: samtools coverage test_samtools_coverage - command: nextflow run ./tests/modules/nf-core/samtools/coverage -entry test_samtools_coverage -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/coverage/nextflow.config + command: nextflow run ./tests/modules/nf-core/samtools/coverage -entry test_samtools_coverage -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/coverage/nextflow.config tags: - samtools/coverage - samtools files: - - path: output/samtools/test.csv - md5sum: 99a521b3bf53b6acf8055a44a571ea84 - path: output/samtools/test.txt - md5sum: 12c231c5720cbbbdc5344db22e6bfabf + md5sum: 99a521b3bf53b6acf8055a44a571ea84 + - path: output/samtools/versions.yml diff --git a/tests/modules/nf-core/samtools/stats/main.nf b/tests/modules/nf-core/samtools/stats/main.nf index 523056a..62aa2fe 100644 --- a/tests/modules/nf-core/samtools/stats/main.nf +++ b/tests/modules/nf-core/samtools/stats/main.nf @@ -10,15 +10,18 @@ workflow test_samtools_stats { file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - SAMTOOLS_STATS ( input, []) + SAMTOOLS_STATS ( input, [[],[]]) } workflow test_samtools_stats_cram { - input = [ [ id: 'test', single_end:true ], // meta map + input = [ [ id: 'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] SAMTOOLS_STATS ( input, fasta ) } diff --git a/tests/modules/nf-core/samtools/stats/test.yml b/tests/modules/nf-core/samtools/stats/test.yml index 819db89..24931e8 100644 --- a/tests/modules/nf-core/samtools/stats/test.yml +++ b/tests/modules/nf-core/samtools/stats/test.yml @@ -5,7 +5,7 @@ - samtools/stats files: - path: output/samtools/test.stats - md5sum: 37b24a161ade89aef4155df6354efa8c + md5sum: 045a48208b1c6f5b8af4347fe31f4def - name: samtools stats test_samtools_stats_cram command: nextflow run ./tests/modules/nf-core/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/stats/nextflow.config @@ -14,4 +14,4 @@ - samtools/stats files: - path: output/samtools/test.stats - md5sum: 7b3cd70d76085eb4a27938e7159daa12 + md5sum: dfbfa130d4a6925ddd1931dcd8354a43 diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/main.nf b/tests/subworkflows/nf-core/bam_stats_samtools/main.nf index 14884fb..5d302d8 100644 --- a/tests/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/tests/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -10,7 +10,10 @@ workflow test_bam_stats_samtools_single_end { file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true) ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fasta = [ + [ id:'genome' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] BAM_STATS_SAMTOOLS ( input, fasta ) } @@ -21,7 +24,10 @@ workflow test_bam_stats_samtools_paired_end { file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fasta = [ + [ id:'genome' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] BAM_STATS_SAMTOOLS ( input, fasta ) } @@ -33,7 +39,10 @@ workflow test_bam_stats_samtools_paired_end_cram { file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] BAM_STATS_SAMTOOLS ( input, fasta ) } diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml index 1325c61..a62de8c 100644 --- a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml +++ b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml @@ -13,7 +13,7 @@ - path: output/samtools/test.idxstats md5sum: 613e048487662c694aa4a2f73ca96a20 - path: output/samtools/test.stats - md5sum: 930cf4e764cfa0ee4f3ca0168442f338 + md5sum: 5a6667d97806e5002731e9cf23674fad - name: bam_stats_samtools test_bam_stats_samtools_paired_end command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c ./tests/config/nextflow.config @@ -30,7 +30,7 @@ - path: output/samtools/test.idxstats md5sum: df60a8c8d6621100d05178c93fb053a2 - path: output/samtools/test.stats - md5sum: 7602d5fc2bc0207cca3f6ee214d1688f + md5sum: 49e2b43344ff92bc4c02463a58f7ba4a - name: bam_stats_samtools test_bam_stats_samtools_paired_end_cram command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end_cram -c ./tests/config/nextflow.config @@ -47,4 +47,4 @@ - path: output/samtools/test.idxstats md5sum: e179601fa7b8ebce81ac3765206f6c15 - path: output/samtools/test.stats - md5sum: fcc070b235a87bc305186bec94cb6bfa + md5sum: 2cf2fe93596ee3d74f946097b204a629 From 60c857edb530b3882b95048f08c0bd93e4d77866 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 18 Dec 2023 15:51:30 +0100 Subject: [PATCH 14/14] :bug: fix freebayes chunk md5 --- tests/modules/cnr-ibba/freebayes/chunk/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/cnr-ibba/freebayes/chunk/test.yml b/tests/modules/cnr-ibba/freebayes/chunk/test.yml index 584656d..3f6d637 100644 --- a/tests/modules/cnr-ibba/freebayes/chunk/test.yml +++ b/tests/modules/cnr-ibba/freebayes/chunk/test.yml @@ -9,6 +9,6 @@ - path: output/freebayes/all.fb.regions.txt md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5 - path: output/freebayes/chr22:0-40001.vcf.gz - md5sum: af568e83b7682a70988b9487f153f54a + md5sum: fba544980eebf86c66460c40f48d7809 - path: output/freebayes/chr22:0-40001.vcf.gz.tbi md5sum: 83b1d5e5b36d61529d9d2d69cd4babc5