🔧 fix configuration stuff

cnr-ibba · Mar 15, 2024 · a182d0d · a182d0d
1 parent 4405d06
commit a182d0d
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Showing 19 changed files with 43 additions and 43 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,29 +1,29 @@
 - 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
   files:
     - 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
   files:
     - 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
   files:
     - 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
@@ -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
@@ -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