From 4405d06441e7a1afc1f0ddd1b337e564e404c0ca Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Mar 2024 13:07:09 +0100 Subject: [PATCH 1/4] :truck: move modules from nf-core to cnr-ibba folder --- modules/{nf-core => cnr-ibba}/bcftools/concat/environment.yml | 0 modules/{nf-core => cnr-ibba}/bcftools/concat/main.nf | 0 modules/{nf-core => cnr-ibba}/bcftools/concat/meta.yml | 0 modules/{nf-core => cnr-ibba}/samtools/coverage/environment.yml | 0 modules/{nf-core => cnr-ibba}/samtools/coverage/main.nf | 0 modules/{nf-core => cnr-ibba}/samtools/coverage/meta.yml | 0 modules/{nf-core => cnr-ibba}/samtools/flagstat/environment.yml | 0 modules/{nf-core => cnr-ibba}/samtools/flagstat/main.nf | 0 modules/{nf-core => cnr-ibba}/samtools/flagstat/meta.yml | 0 modules/{nf-core => cnr-ibba}/samtools/idxstats/environment.yml | 0 modules/{nf-core => cnr-ibba}/samtools/idxstats/main.nf | 0 modules/{nf-core => cnr-ibba}/samtools/idxstats/meta.yml | 0 .../{nf-core => cnr-ibba}/samtools/idxstats/tests/main.nf.test | 0 .../samtools/idxstats/tests/main.nf.test.snap | 0 modules/{nf-core => cnr-ibba}/samtools/idxstats/tests/tags.yml | 0 modules/{nf-core => cnr-ibba}/samtools/stats/environment.yml | 0 modules/{nf-core => cnr-ibba}/samtools/stats/main.nf | 0 modules/{nf-core => cnr-ibba}/samtools/stats/meta.yml | 0 modules/{nf-core => cnr-ibba}/tabix/tabix/environment.yml | 0 modules/{nf-core => cnr-ibba}/tabix/tabix/main.nf | 0 modules/{nf-core => cnr-ibba}/tabix/tabix/meta.yml | 0 subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/main.nf | 0 subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/meta.yml | 0 .../{nf-core => cnr-ibba}/bam_stats_samtools/tests/main.nf.test | 0 .../bam_stats_samtools/tests/main.nf.test.snap | 0 .../{nf-core => cnr-ibba}/bam_stats_samtools/tests/tags.yml | 0 tests/modules/{nf-core => cnr-ibba}/bcftools/concat/main.nf | 0 .../modules/{nf-core => cnr-ibba}/bcftools/concat/nextflow.config | 0 tests/modules/{nf-core => cnr-ibba}/bcftools/concat/test.yml | 0 tests/modules/{nf-core => cnr-ibba}/samtools/coverage/main.nf | 0 .../{nf-core => cnr-ibba}/samtools/coverage/nextflow.config | 0 tests/modules/{nf-core => cnr-ibba}/samtools/coverage/test.yml | 0 tests/modules/{nf-core => cnr-ibba}/samtools/flagstat/main.nf | 0 .../{nf-core => cnr-ibba}/samtools/flagstat/nextflow.config | 0 tests/modules/{nf-core => cnr-ibba}/samtools/flagstat/test.yml | 0 tests/modules/{nf-core => cnr-ibba}/samtools/idxstats/main.nf | 0 .../{nf-core => cnr-ibba}/samtools/idxstats/nextflow.config | 0 tests/modules/{nf-core => cnr-ibba}/samtools/idxstats/test.yml | 0 tests/modules/{nf-core => cnr-ibba}/samtools/stats/main.nf | 0 .../modules/{nf-core => cnr-ibba}/samtools/stats/nextflow.config | 0 tests/modules/{nf-core => cnr-ibba}/samtools/stats/test.yml | 0 tests/modules/{nf-core => cnr-ibba}/tabix/tabix/main.nf | 0 tests/modules/{nf-core => cnr-ibba}/tabix/tabix/nextflow.config | 0 tests/modules/{nf-core => cnr-ibba}/tabix/tabix/test.yml | 0 .../subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/main.nf | 0 .../{nf-core => cnr-ibba}/bam_stats_samtools/nextflow.config | 0 .../{nf-core => cnr-ibba}/bam_stats_samtools/test.yml | 0 47 files changed, 0 insertions(+), 0 deletions(-) rename modules/{nf-core => cnr-ibba}/bcftools/concat/environment.yml (100%) rename modules/{nf-core => cnr-ibba}/bcftools/concat/main.nf (100%) rename modules/{nf-core => cnr-ibba}/bcftools/concat/meta.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/coverage/environment.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/coverage/main.nf (100%) rename modules/{nf-core => cnr-ibba}/samtools/coverage/meta.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/flagstat/environment.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/flagstat/main.nf (100%) rename modules/{nf-core => cnr-ibba}/samtools/flagstat/meta.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/idxstats/environment.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/idxstats/main.nf (100%) rename modules/{nf-core => cnr-ibba}/samtools/idxstats/meta.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/idxstats/tests/main.nf.test (100%) rename modules/{nf-core => cnr-ibba}/samtools/idxstats/tests/main.nf.test.snap (100%) rename modules/{nf-core => cnr-ibba}/samtools/idxstats/tests/tags.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/stats/environment.yml (100%) rename modules/{nf-core => cnr-ibba}/samtools/stats/main.nf (100%) rename modules/{nf-core => cnr-ibba}/samtools/stats/meta.yml (100%) rename modules/{nf-core => cnr-ibba}/tabix/tabix/environment.yml (100%) rename modules/{nf-core => cnr-ibba}/tabix/tabix/main.nf (100%) rename modules/{nf-core => cnr-ibba}/tabix/tabix/meta.yml (100%) rename subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/main.nf (100%) rename subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/meta.yml (100%) rename subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/tests/main.nf.test (100%) rename subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/tests/main.nf.test.snap (100%) rename subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/tests/tags.yml (100%) rename tests/modules/{nf-core => cnr-ibba}/bcftools/concat/main.nf (100%) rename tests/modules/{nf-core => cnr-ibba}/bcftools/concat/nextflow.config (100%) rename tests/modules/{nf-core => cnr-ibba}/bcftools/concat/test.yml (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/coverage/main.nf (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/coverage/nextflow.config (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/coverage/test.yml (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/flagstat/main.nf (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/flagstat/nextflow.config (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/flagstat/test.yml (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/idxstats/main.nf (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/idxstats/nextflow.config (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/idxstats/test.yml (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/stats/main.nf (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/stats/nextflow.config (100%) rename tests/modules/{nf-core => cnr-ibba}/samtools/stats/test.yml (100%) rename tests/modules/{nf-core => cnr-ibba}/tabix/tabix/main.nf (100%) rename tests/modules/{nf-core => cnr-ibba}/tabix/tabix/nextflow.config (100%) rename tests/modules/{nf-core => cnr-ibba}/tabix/tabix/test.yml (100%) rename tests/subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/main.nf (100%) rename tests/subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/nextflow.config (100%) rename tests/subworkflows/{nf-core => cnr-ibba}/bam_stats_samtools/test.yml (100%) diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/cnr-ibba/bcftools/concat/environment.yml similarity index 100% rename from modules/nf-core/bcftools/concat/environment.yml rename to modules/cnr-ibba/bcftools/concat/environment.yml diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/cnr-ibba/bcftools/concat/main.nf similarity index 100% rename from modules/nf-core/bcftools/concat/main.nf rename to modules/cnr-ibba/bcftools/concat/main.nf diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/cnr-ibba/bcftools/concat/meta.yml similarity index 100% rename from modules/nf-core/bcftools/concat/meta.yml rename to modules/cnr-ibba/bcftools/concat/meta.yml diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/cnr-ibba/samtools/coverage/environment.yml similarity index 100% rename from modules/nf-core/samtools/coverage/environment.yml rename to modules/cnr-ibba/samtools/coverage/environment.yml diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/cnr-ibba/samtools/coverage/main.nf similarity index 100% rename from modules/nf-core/samtools/coverage/main.nf rename to modules/cnr-ibba/samtools/coverage/main.nf diff --git a/modules/nf-core/samtools/coverage/meta.yml b/modules/cnr-ibba/samtools/coverage/meta.yml similarity index 100% rename from modules/nf-core/samtools/coverage/meta.yml rename to modules/cnr-ibba/samtools/coverage/meta.yml diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/cnr-ibba/samtools/flagstat/environment.yml similarity index 100% rename from modules/nf-core/samtools/flagstat/environment.yml rename to modules/cnr-ibba/samtools/flagstat/environment.yml diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/cnr-ibba/samtools/flagstat/main.nf similarity index 100% rename from modules/nf-core/samtools/flagstat/main.nf rename to modules/cnr-ibba/samtools/flagstat/main.nf diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/cnr-ibba/samtools/flagstat/meta.yml similarity index 100% rename from modules/nf-core/samtools/flagstat/meta.yml rename to modules/cnr-ibba/samtools/flagstat/meta.yml diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/cnr-ibba/samtools/idxstats/environment.yml similarity index 100% rename from modules/nf-core/samtools/idxstats/environment.yml rename to modules/cnr-ibba/samtools/idxstats/environment.yml diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/cnr-ibba/samtools/idxstats/main.nf similarity index 100% rename from modules/nf-core/samtools/idxstats/main.nf rename to modules/cnr-ibba/samtools/idxstats/main.nf diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/cnr-ibba/samtools/idxstats/meta.yml similarity index 100% rename from modules/nf-core/samtools/idxstats/meta.yml rename to modules/cnr-ibba/samtools/idxstats/meta.yml diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/cnr-ibba/samtools/idxstats/tests/main.nf.test similarity index 100% rename from modules/nf-core/samtools/idxstats/tests/main.nf.test rename to modules/cnr-ibba/samtools/idxstats/tests/main.nf.test diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/cnr-ibba/samtools/idxstats/tests/main.nf.test.snap similarity index 100% rename from modules/nf-core/samtools/idxstats/tests/main.nf.test.snap rename to modules/cnr-ibba/samtools/idxstats/tests/main.nf.test.snap diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/cnr-ibba/samtools/idxstats/tests/tags.yml similarity index 100% rename from modules/nf-core/samtools/idxstats/tests/tags.yml rename to modules/cnr-ibba/samtools/idxstats/tests/tags.yml diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/cnr-ibba/samtools/stats/environment.yml similarity index 100% rename from modules/nf-core/samtools/stats/environment.yml rename to modules/cnr-ibba/samtools/stats/environment.yml diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/cnr-ibba/samtools/stats/main.nf similarity index 100% rename from modules/nf-core/samtools/stats/main.nf rename to modules/cnr-ibba/samtools/stats/main.nf diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/cnr-ibba/samtools/stats/meta.yml similarity index 100% rename from modules/nf-core/samtools/stats/meta.yml rename to modules/cnr-ibba/samtools/stats/meta.yml diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/cnr-ibba/tabix/tabix/environment.yml similarity index 100% rename from modules/nf-core/tabix/tabix/environment.yml rename to modules/cnr-ibba/tabix/tabix/environment.yml diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/cnr-ibba/tabix/tabix/main.nf similarity index 100% rename from modules/nf-core/tabix/tabix/main.nf rename to modules/cnr-ibba/tabix/tabix/main.nf diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/cnr-ibba/tabix/tabix/meta.yml similarity index 100% rename from modules/nf-core/tabix/tabix/meta.yml rename to modules/cnr-ibba/tabix/tabix/meta.yml diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/cnr-ibba/bam_stats_samtools/main.nf similarity index 100% rename from subworkflows/nf-core/bam_stats_samtools/main.nf rename to subworkflows/cnr-ibba/bam_stats_samtools/main.nf diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/cnr-ibba/bam_stats_samtools/meta.yml similarity index 100% rename from subworkflows/nf-core/bam_stats_samtools/meta.yml rename to subworkflows/cnr-ibba/bam_stats_samtools/meta.yml diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/cnr-ibba/bam_stats_samtools/tests/main.nf.test similarity index 100% rename from subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test rename to subworkflows/cnr-ibba/bam_stats_samtools/tests/main.nf.test diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/cnr-ibba/bam_stats_samtools/tests/main.nf.test.snap similarity index 100% rename from subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap rename to subworkflows/cnr-ibba/bam_stats_samtools/tests/main.nf.test.snap diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml similarity index 100% rename from subworkflows/nf-core/bam_stats_samtools/tests/tags.yml rename to subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml diff --git a/tests/modules/nf-core/bcftools/concat/main.nf b/tests/modules/cnr-ibba/bcftools/concat/main.nf similarity index 100% rename from tests/modules/nf-core/bcftools/concat/main.nf rename to tests/modules/cnr-ibba/bcftools/concat/main.nf diff --git a/tests/modules/nf-core/bcftools/concat/nextflow.config b/tests/modules/cnr-ibba/bcftools/concat/nextflow.config similarity index 100% rename from tests/modules/nf-core/bcftools/concat/nextflow.config rename to tests/modules/cnr-ibba/bcftools/concat/nextflow.config diff --git a/tests/modules/nf-core/bcftools/concat/test.yml b/tests/modules/cnr-ibba/bcftools/concat/test.yml similarity index 100% rename from tests/modules/nf-core/bcftools/concat/test.yml rename to tests/modules/cnr-ibba/bcftools/concat/test.yml diff --git a/tests/modules/nf-core/samtools/coverage/main.nf b/tests/modules/cnr-ibba/samtools/coverage/main.nf similarity index 100% rename from tests/modules/nf-core/samtools/coverage/main.nf rename to tests/modules/cnr-ibba/samtools/coverage/main.nf diff --git a/tests/modules/nf-core/samtools/coverage/nextflow.config b/tests/modules/cnr-ibba/samtools/coverage/nextflow.config similarity index 100% rename from tests/modules/nf-core/samtools/coverage/nextflow.config rename to tests/modules/cnr-ibba/samtools/coverage/nextflow.config diff --git a/tests/modules/nf-core/samtools/coverage/test.yml b/tests/modules/cnr-ibba/samtools/coverage/test.yml similarity index 100% rename from tests/modules/nf-core/samtools/coverage/test.yml rename to tests/modules/cnr-ibba/samtools/coverage/test.yml diff --git a/tests/modules/nf-core/samtools/flagstat/main.nf b/tests/modules/cnr-ibba/samtools/flagstat/main.nf similarity index 100% rename from tests/modules/nf-core/samtools/flagstat/main.nf rename to tests/modules/cnr-ibba/samtools/flagstat/main.nf diff --git a/tests/modules/nf-core/samtools/flagstat/nextflow.config b/tests/modules/cnr-ibba/samtools/flagstat/nextflow.config similarity index 100% rename from tests/modules/nf-core/samtools/flagstat/nextflow.config rename to tests/modules/cnr-ibba/samtools/flagstat/nextflow.config diff --git a/tests/modules/nf-core/samtools/flagstat/test.yml b/tests/modules/cnr-ibba/samtools/flagstat/test.yml similarity index 100% rename from tests/modules/nf-core/samtools/flagstat/test.yml rename to tests/modules/cnr-ibba/samtools/flagstat/test.yml diff --git a/tests/modules/nf-core/samtools/idxstats/main.nf b/tests/modules/cnr-ibba/samtools/idxstats/main.nf similarity index 100% rename from tests/modules/nf-core/samtools/idxstats/main.nf rename to tests/modules/cnr-ibba/samtools/idxstats/main.nf diff --git a/tests/modules/nf-core/samtools/idxstats/nextflow.config b/tests/modules/cnr-ibba/samtools/idxstats/nextflow.config similarity index 100% rename from tests/modules/nf-core/samtools/idxstats/nextflow.config rename to tests/modules/cnr-ibba/samtools/idxstats/nextflow.config diff --git a/tests/modules/nf-core/samtools/idxstats/test.yml b/tests/modules/cnr-ibba/samtools/idxstats/test.yml similarity index 100% rename from tests/modules/nf-core/samtools/idxstats/test.yml rename to tests/modules/cnr-ibba/samtools/idxstats/test.yml diff --git a/tests/modules/nf-core/samtools/stats/main.nf b/tests/modules/cnr-ibba/samtools/stats/main.nf similarity index 100% rename from tests/modules/nf-core/samtools/stats/main.nf rename to tests/modules/cnr-ibba/samtools/stats/main.nf diff --git a/tests/modules/nf-core/samtools/stats/nextflow.config b/tests/modules/cnr-ibba/samtools/stats/nextflow.config similarity index 100% rename from tests/modules/nf-core/samtools/stats/nextflow.config rename to tests/modules/cnr-ibba/samtools/stats/nextflow.config diff --git a/tests/modules/nf-core/samtools/stats/test.yml b/tests/modules/cnr-ibba/samtools/stats/test.yml similarity index 100% rename from tests/modules/nf-core/samtools/stats/test.yml rename to tests/modules/cnr-ibba/samtools/stats/test.yml diff --git a/tests/modules/nf-core/tabix/tabix/main.nf b/tests/modules/cnr-ibba/tabix/tabix/main.nf similarity index 100% rename from tests/modules/nf-core/tabix/tabix/main.nf rename to tests/modules/cnr-ibba/tabix/tabix/main.nf diff --git a/tests/modules/nf-core/tabix/tabix/nextflow.config b/tests/modules/cnr-ibba/tabix/tabix/nextflow.config similarity index 100% rename from tests/modules/nf-core/tabix/tabix/nextflow.config rename to tests/modules/cnr-ibba/tabix/tabix/nextflow.config diff --git a/tests/modules/nf-core/tabix/tabix/test.yml b/tests/modules/cnr-ibba/tabix/tabix/test.yml similarity index 100% rename from tests/modules/nf-core/tabix/tabix/test.yml rename to tests/modules/cnr-ibba/tabix/tabix/test.yml diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/main.nf b/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf similarity index 100% rename from tests/subworkflows/nf-core/bam_stats_samtools/main.nf rename to tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config b/tests/subworkflows/cnr-ibba/bam_stats_samtools/nextflow.config similarity index 100% rename from tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config rename to tests/subworkflows/cnr-ibba/bam_stats_samtools/nextflow.config diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml b/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml similarity index 100% rename from tests/subworkflows/nf-core/bam_stats_samtools/test.yml rename to tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml From a182d0d16206a756877bd9d0260fa9fe22d46bb8 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Mar 2024 13:12:03 +0100 Subject: [PATCH 2/4] :wrench: fix configuration stuff --- .../cnr-ibba/samtools/idxstats/tests/tags.yml | 2 +- .../cnr-ibba/bam_stats_samtools/main.nf | 6 ++--- .../bam_stats_samtools/tests/tags.yml | 2 +- .../cnr-ibba/freebayes_parallel/main.nf | 4 ++-- tests/config/pytest_modules.yml | 24 +++++++++---------- .../modules/cnr-ibba/bcftools/concat/main.nf | 2 +- .../modules/cnr-ibba/bcftools/concat/test.yml | 4 ++-- .../cnr-ibba/samtools/coverage/main.nf | 2 +- .../cnr-ibba/samtools/coverage/test.yml | 2 +- .../cnr-ibba/samtools/flagstat/main.nf | 2 +- .../cnr-ibba/samtools/flagstat/test.yml | 2 +- .../cnr-ibba/samtools/idxstats/main.nf | 2 +- .../cnr-ibba/samtools/idxstats/test.yml | 2 +- tests/modules/cnr-ibba/samtools/stats/main.nf | 2 +- .../modules/cnr-ibba/samtools/stats/test.yml | 4 ++-- tests/modules/cnr-ibba/tabix/tabix/main.nf | 8 +++---- tests/modules/cnr-ibba/tabix/tabix/test.yml | 8 +++---- .../cnr-ibba/bam_stats_samtools/main.nf | 2 +- .../cnr-ibba/bam_stats_samtools/test.yml | 6 ++--- 19 files changed, 43 insertions(+), 43 deletions(-) diff --git a/modules/cnr-ibba/samtools/idxstats/tests/tags.yml b/modules/cnr-ibba/samtools/idxstats/tests/tags.yml index d3057c6..4aea3a8 100644 --- a/modules/cnr-ibba/samtools/idxstats/tests/tags.yml +++ b/modules/cnr-ibba/samtools/idxstats/tests/tags.yml @@ -1,2 +1,2 @@ samtools/idxstats: - - modules/nf-core/samtools/idxstats/** + - modules/cnr-ibba/samtools/idxstats/** diff --git a/subworkflows/cnr-ibba/bam_stats_samtools/main.nf b/subworkflows/cnr-ibba/bam_stats_samtools/main.nf index 44d4c01..d27e9c4 100644 --- a/subworkflows/cnr-ibba/bam_stats_samtools/main.nf +++ b/subworkflows/cnr-ibba/bam_stats_samtools/main.nf @@ -2,9 +2,9 @@ // Run SAMtools stats, flagstat and idxstats // -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' +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' workflow BAM_STATS_SAMTOOLS { take: diff --git a/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml b/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml index ec2f2d6..fbbc592 100644 --- a/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml +++ b/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml @@ -1,2 +1,2 @@ subworkflows/bam_stats_samtools: - - subworkflows/nf-core/bam_stats_samtools/** + - subworkflows/cnr-ibba/bam_stats_samtools/** diff --git a/subworkflows/cnr-ibba/freebayes_parallel/main.nf b/subworkflows/cnr-ibba/freebayes_parallel/main.nf index 6aaa108..44f6e5d 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/nf-core/bcftools/concat/main' -include { TABIX_TABIX as FREEBAYES_TABIX } from '../../../modules/nf-core/tabix/tabix/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' workflow FREEBAYES_PARALLEL { take: diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 078c934..d21b94f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -7,8 +7,8 @@ bamtools/coverage: - tests/modules/cnr-ibba/bamtools/coverage/** bcftools/concat: - - modules/nf-core/bcftools/concat/** - - tests/modules/nf-core/bcftools/concat/** + - modules/cnr-ibba/bcftools/concat/** + - tests/modules/cnr-ibba/bcftools/concat/** estsfs: - modules/cnr-ibba/estsfs/** @@ -31,25 +31,25 @@ freebayes/splitbam: - tests/modules/cnr-ibba/freebayes/splitbam/** samtools/coverage: - - modules/nf-core/samtools/coverage/** - - tests/modules/nf-core/samtools/coverage/** + - modules/cnr-ibba/samtools/coverage/** + - tests/modules/cnr-ibba/samtools/coverage/** samtools/flagstat: - - modules/nf-core/samtools/flagstat/** - - tests/modules/nf-core/samtools/flagstat/** + - modules/cnr-ibba/samtools/flagstat/** + - tests/modules/cnr-ibba/samtools/flagstat/** samtools/idxstats: - - modules/nf-core/samtools/idxstats/** - - tests/modules/nf-core/samtools/idxstats/** + - modules/cnr-ibba/samtools/idxstats/** + - tests/modules/cnr-ibba/samtools/idxstats/** samtools/stats: - - modules/nf-core/samtools/stats/** - - tests/modules/nf-core/samtools/stats/** + - modules/cnr-ibba/samtools/stats/** + - tests/modules/cnr-ibba/samtools/stats/** seqkit/rmdup: - modules/cnr-ibba/seqkit/rmdup/** - tests/modules/cnr-ibba/seqkit/rmdup/** tabix/tabix: - - modules/nf-core/tabix/tabix/** - - tests/modules/nf-core/tabix/tabix/** + - modules/cnr-ibba/tabix/tabix/** + - tests/modules/cnr-ibba/tabix/tabix/** diff --git a/tests/modules/cnr-ibba/bcftools/concat/main.nf b/tests/modules/cnr-ibba/bcftools/concat/main.nf index 49960a9..6e12d12 100644 --- a/tests/modules/cnr-ibba/bcftools/concat/main.nf +++ b/tests/modules/cnr-ibba/bcftools/concat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BCFTOOLS_CONCAT } from '../../../../../modules/nf-core/bcftools/concat/main.nf' +include { BCFTOOLS_CONCAT } from '../../../../../modules/cnr-ibba/bcftools/concat/main.nf' workflow test_bcftools_concat_tbi { diff --git a/tests/modules/cnr-ibba/bcftools/concat/test.yml b/tests/modules/cnr-ibba/bcftools/concat/test.yml index 4ea393f..1a4d441 100644 --- a/tests/modules/cnr-ibba/bcftools/concat/test.yml +++ b/tests/modules/cnr-ibba/bcftools/concat/test.yml @@ -1,5 +1,5 @@ - name: bcftools concat test_bcftools_concat_tbi - 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 + 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 tags: - bcftools - bcftools/concat @@ -8,7 +8,7 @@ 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 + 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 tags: - bcftools - bcftools/concat diff --git a/tests/modules/cnr-ibba/samtools/coverage/main.nf b/tests/modules/cnr-ibba/samtools/coverage/main.nf index a4a7ce4..d847402 100644 --- a/tests/modules/cnr-ibba/samtools/coverage/main.nf +++ b/tests/modules/cnr-ibba/samtools/coverage/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_COVERAGE } from '../../../../../modules/nf-core/samtools/coverage/main.nf' +include { SAMTOOLS_COVERAGE } from '../../../../../modules/cnr-ibba/samtools/coverage/main.nf' workflow test_samtools_coverage { input = [ [ id:'test', single_end:false ], // meta map diff --git a/tests/modules/cnr-ibba/samtools/coverage/test.yml b/tests/modules/cnr-ibba/samtools/coverage/test.yml index 9e57de9..1eecc31 100644 --- a/tests/modules/cnr-ibba/samtools/coverage/test.yml +++ b/tests/modules/cnr-ibba/samtools/coverage/test.yml @@ -1,5 +1,5 @@ - 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/cnr-ibba/samtools/coverage -entry test_samtools_coverage -c ./tests/config/nextflow.config -c ./tests/modules/cnr-ibba/samtools/coverage/nextflow.config tags: - samtools/coverage - samtools diff --git a/tests/modules/cnr-ibba/samtools/flagstat/main.nf b/tests/modules/cnr-ibba/samtools/flagstat/main.nf index c1a435f..4dc6d56 100644 --- a/tests/modules/cnr-ibba/samtools/flagstat/main.nf +++ b/tests/modules/cnr-ibba/samtools/flagstat/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_FLAGSTAT } from '../../../../../modules/nf-core/samtools/flagstat/main.nf' +include { SAMTOOLS_FLAGSTAT } from '../../../../../modules/cnr-ibba/samtools/flagstat/main.nf' workflow test_samtools_flagstat { input = [ diff --git a/tests/modules/cnr-ibba/samtools/flagstat/test.yml b/tests/modules/cnr-ibba/samtools/flagstat/test.yml index ad58ad5..3dc63cc 100644 --- a/tests/modules/cnr-ibba/samtools/flagstat/test.yml +++ b/tests/modules/cnr-ibba/samtools/flagstat/test.yml @@ -1,5 +1,5 @@ - name: samtools flagstat test_samtools_flagstat - 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 + 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 tags: - samtools/flagstat - samtools diff --git a/tests/modules/cnr-ibba/samtools/idxstats/main.nf b/tests/modules/cnr-ibba/samtools/idxstats/main.nf index 4a29252..34d4804 100644 --- a/tests/modules/cnr-ibba/samtools/idxstats/main.nf +++ b/tests/modules/cnr-ibba/samtools/idxstats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_IDXSTATS } from '../../../../../modules/nf-core/samtools/idxstats/main.nf' +include { SAMTOOLS_IDXSTATS } from '../../../../../modules/cnr-ibba/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/test.yml b/tests/modules/cnr-ibba/samtools/idxstats/test.yml index 8c596c2..6a9f1ed 100644 --- a/tests/modules/cnr-ibba/samtools/idxstats/test.yml +++ b/tests/modules/cnr-ibba/samtools/idxstats/test.yml @@ -1,5 +1,5 @@ - name: samtools idxstats test_samtools_idxstats - 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 + 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 tags: - samtools/idxstats - samtools diff --git a/tests/modules/cnr-ibba/samtools/stats/main.nf b/tests/modules/cnr-ibba/samtools/stats/main.nf index 62aa2fe..2b36092 100644 --- a/tests/modules/cnr-ibba/samtools/stats/main.nf +++ b/tests/modules/cnr-ibba/samtools/stats/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { SAMTOOLS_STATS } from '../../../../../modules/nf-core/samtools/stats/main.nf' +include { SAMTOOLS_STATS } from '../../../../../modules/cnr-ibba/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/test.yml b/tests/modules/cnr-ibba/samtools/stats/test.yml index 24931e8..bc8a608 100644 --- a/tests/modules/cnr-ibba/samtools/stats/test.yml +++ b/tests/modules/cnr-ibba/samtools/stats/test.yml @@ -1,5 +1,5 @@ - name: samtools stats test_samtools_stats - 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 + 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 tags: - samtools - samtools/stats @@ -8,7 +8,7 @@ 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 + 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 tags: - samtools - samtools/stats diff --git a/tests/modules/cnr-ibba/tabix/tabix/main.nf b/tests/modules/cnr-ibba/tabix/tabix/main.nf index 31b78e0..ad2c57d 100644 --- a/tests/modules/cnr-ibba/tabix/tabix/main.nf +++ b/tests/modules/cnr-ibba/tabix/tabix/main.nf @@ -2,10 +2,10 @@ nextflow.enable.dsl = 2 -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' +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' workflow test_tabix_tabix_bed { input = [ [ id:'B.bed' ], // meta map diff --git a/tests/modules/cnr-ibba/tabix/tabix/test.yml b/tests/modules/cnr-ibba/tabix/tabix/test.yml index 5a2fb2d..b8b3ade 100644 --- a/tests/modules/cnr-ibba/tabix/tabix/test.yml +++ b/tests/modules/cnr-ibba/tabix/tabix/test.yml @@ -1,5 +1,5 @@ - name: tabix tabix bed - 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 + 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 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/nf-core/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tabix/tabix/nextflow.config + 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 tags: - tabix - tabix/tabix @@ -15,7 +15,7 @@ - path: ./output/tabix/genome.gff3.gz.tbi md5sum: f79a67d95a98076e04fbe0455d825926 - name: tabix tabix vcf - 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 + 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 tags: - tabix - tabix/tabix @@ -23,7 +23,7 @@ - path: output/tabix/test.vcf.gz.tbi md5sum: d22e5b84e4fcd18792179f72e6da702e - name: tabix tabix vcf csi - 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 + 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 tags: - tabix - tabix/tabix diff --git a/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf b/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf index 5d302d8..ecff8a4 100644 --- a/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf +++ b/tests/subworkflows/cnr-ibba/bam_stats_samtools/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { BAM_STATS_SAMTOOLS } from '../../../../subworkflows/nf-core/bam_stats_samtools/main' +include { BAM_STATS_SAMTOOLS } from '../../../../subworkflows/cnr-ibba/bam_stats_samtools/main' workflow test_bam_stats_samtools_single_end { input = [ diff --git a/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml b/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml index a62de8c..381a0fa 100644 --- a/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml +++ b/tests/subworkflows/cnr-ibba/bam_stats_samtools/test.yml @@ -1,5 +1,5 @@ - name: bam_stats_samtools test_bam_stats_samtools_single_end - command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c ./tests/config/nextflow.config + command: nextflow run ./tests/subworkflows/cnr-ibba/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c ./tests/config/nextflow.config tags: - samtools - samtools/flagstat @@ -16,7 +16,7 @@ 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 + command: nextflow run ./tests/subworkflows/cnr-ibba/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c ./tests/config/nextflow.config tags: - samtools - samtools/flagstat @@ -33,7 +33,7 @@ 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 + command: nextflow run ./tests/subworkflows/cnr-ibba/bam_stats_samtools -entry test_bam_stats_samtools_paired_end_cram -c ./tests/config/nextflow.config tags: - samtools - samtools/flagstat From 95149a87b277cfda4bbb8508ca68281984a74605 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Mar 2024 13:29:14 +0100 Subject: [PATCH 3/4] :green_heart: attempt to fix pytest configuration --- pytest.ini | 2 -- 1 file changed, 2 deletions(-) diff --git a/pytest.ini b/pytest.ini index 02a8aca..eea2c18 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,3 +1 @@ [pytest] -filterwarnings = - ignore::pytest.PytestRemovedIn8Warning:_pytest.nodes:140 From c3831b4a7ae793e6fdd7f2d64a85677ff793e48d Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 15 Mar 2024 13:36:35 +0100 Subject: [PATCH 4/4] :construction_worker: update CI actions --- .github/workflows/pytest-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index fc92743..fa9697e 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -72,13 +72,13 @@ jobs: - name: Set up Singularity if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-singularity@v5 + uses: eWaterCycle/setup-singularity@v7 with: singularity-version: 3.7.1 - name: Set up miniconda if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true channels: conda-forge,bioconda,defaults