cnr-ibba · bunop · Mar 15, 2024 · Mar 15, 2024 · Mar 15, 2024 · Mar 15, 2024
diff --git 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

diff --git a/...s/nf-core/bcftools/concat/environment.yml → .../cnr-ibba/bcftools/concat/environment.yml b/...s/nf-core/bcftools/concat/environment.yml → .../cnr-ibba/bcftools/concat/environment.yml
diff --git a/modules/nf-core/bcftools/concat/main.nf → modules/cnr-ibba/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf → modules/cnr-ibba/bcftools/concat/main.nf
diff --git a/modules/nf-core/bcftools/concat/meta.yml → modules/cnr-ibba/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml → modules/cnr-ibba/bcftools/concat/meta.yml
diff --git a/...nf-core/samtools/coverage/environment.yml → ...nr-ibba/samtools/coverage/environment.yml b/...nf-core/samtools/coverage/environment.yml → ...nr-ibba/samtools/coverage/environment.yml
diff --git a/modules/nf-core/samtools/coverage/main.nf → modules/cnr-ibba/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf → modules/cnr-ibba/samtools/coverage/main.nf
diff --git a/modules/nf-core/samtools/coverage/meta.yml → modules/cnr-ibba/samtools/coverage/meta.yml b/modules/nf-core/samtools/coverage/meta.yml → modules/cnr-ibba/samtools/coverage/meta.yml
diff --git a/...nf-core/samtools/flagstat/environment.yml → ...nr-ibba/samtools/flagstat/environment.yml b/...nf-core/samtools/flagstat/environment.yml → ...nr-ibba/samtools/flagstat/environment.yml
diff --git a/modules/nf-core/samtools/flagstat/main.nf → modules/cnr-ibba/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf → modules/cnr-ibba/samtools/flagstat/main.nf
diff --git a/modules/nf-core/samtools/flagstat/meta.yml → modules/cnr-ibba/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml → modules/cnr-ibba/samtools/flagstat/meta.yml
diff --git a/...nf-core/samtools/idxstats/environment.yml → ...nr-ibba/samtools/idxstats/environment.yml b/...nf-core/samtools/idxstats/environment.yml → ...nr-ibba/samtools/idxstats/environment.yml
diff --git a/modules/nf-core/samtools/idxstats/main.nf → modules/cnr-ibba/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf → modules/cnr-ibba/samtools/idxstats/main.nf
diff --git a/modules/nf-core/samtools/idxstats/meta.yml → modules/cnr-ibba/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml → modules/cnr-ibba/samtools/idxstats/meta.yml
diff --git a/...core/samtools/idxstats/tests/main.nf.test → ...ibba/samtools/idxstats/tests/main.nf.test b/...core/samtools/idxstats/tests/main.nf.test → ...ibba/samtools/idxstats/tests/main.nf.test
diff --git a/...samtools/idxstats/tests/main.nf.test.snap → ...samtools/idxstats/tests/main.nf.test.snap b/...samtools/idxstats/tests/main.nf.test.snap → ...samtools/idxstats/tests/main.nf.test.snap
diff --git a/modules/cnr-ibba/samtools/idxstats/tests/tags.yml b/modules/cnr-ibba/samtools/idxstats/tests/tags.yml
@@ -0,0 +1,2 @@
+samtools/idxstats:
+  - modules/cnr-ibba/samtools/idxstats/**
diff --git a/...es/nf-core/samtools/stats/environment.yml → ...s/cnr-ibba/samtools/stats/environment.yml b/...es/nf-core/samtools/stats/environment.yml → ...s/cnr-ibba/samtools/stats/environment.yml
diff --git a/modules/nf-core/samtools/stats/main.nf → modules/cnr-ibba/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf → modules/cnr-ibba/samtools/stats/main.nf
diff --git a/modules/nf-core/samtools/stats/meta.yml → modules/cnr-ibba/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml → modules/cnr-ibba/samtools/stats/meta.yml
diff --git a/modules/nf-core/tabix/tabix/environment.yml → modules/cnr-ibba/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml → modules/cnr-ibba/tabix/tabix/environment.yml
diff --git a/modules/nf-core/tabix/tabix/main.nf → modules/cnr-ibba/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf → modules/cnr-ibba/tabix/tabix/main.nf
diff --git a/modules/nf-core/tabix/tabix/meta.yml → modules/cnr-ibba/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml → modules/cnr-ibba/tabix/tabix/meta.yml
diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml
diff --git a/pytest.ini b/pytest.ini
@@ -1,3 +1 @@
 [pytest]
-filterwarnings =
-    ignore::pytest.PytestRemovedIn8Warning:_pytest.nodes:140
diff --git a/...kflows/nf-core/bam_stats_samtools/main.nf → ...flows/cnr-ibba/bam_stats_samtools/main.nf b/...kflows/nf-core/bam_stats_samtools/main.nf → ...flows/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/...flows/nf-core/bam_stats_samtools/meta.yml → ...lows/cnr-ibba/bam_stats_samtools/meta.yml b/...flows/nf-core/bam_stats_samtools/meta.yml → ...lows/cnr-ibba/bam_stats_samtools/meta.yml
diff --git a/...ore/bam_stats_samtools/tests/main.nf.test → ...bba/bam_stats_samtools/tests/main.nf.test b/...ore/bam_stats_samtools/tests/main.nf.test → ...bba/bam_stats_samtools/tests/main.nf.test
diff --git a/...am_stats_samtools/tests/main.nf.test.snap → ...am_stats_samtools/tests/main.nf.test.snap b/...am_stats_samtools/tests/main.nf.test.snap → ...am_stats_samtools/tests/main.nf.test.snap
diff --git a/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml b/subworkflows/cnr-ibba/bam_stats_samtools/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/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/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml
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/...s/modules/nf-core/bcftools/concat/main.nf → .../modules/cnr-ibba/bcftools/concat/main.nf b/...s/modules/nf-core/bcftools/concat/main.nf → .../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/...s/nf-core/bcftools/concat/nextflow.config → .../cnr-ibba/bcftools/concat/nextflow.config b/...s/nf-core/bcftools/concat/nextflow.config → .../cnr-ibba/bcftools/concat/nextflow.config
diff --git a/tests/modules/cnr-ibba/bcftools/concat/test.yml b/tests/modules/cnr-ibba/bcftools/concat/test.yml
@@ -0,0 +1,17 @@
+- 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
+  tags:
+    - bcftools
+    - bcftools/concat
+  files:
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: 4bcd0afd89f56c5d433f6b6abc44d0a6
+
+- 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
+  tags:
+    - bcftools
+    - bcftools/concat
+  files:
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: 4bcd0afd89f56c5d433f6b6abc44d0a6
diff --git a/...modules/nf-core/samtools/coverage/main.nf → ...odules/cnr-ibba/samtools/coverage/main.nf b/...modules/nf-core/samtools/coverage/main.nf → ...odules/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/...nf-core/samtools/coverage/nextflow.config → ...nr-ibba/samtools/coverage/nextflow.config b/...nf-core/samtools/coverage/nextflow.config → ...nr-ibba/samtools/coverage/nextflow.config
diff --git a/...odules/nf-core/samtools/coverage/test.yml → ...dules/cnr-ibba/samtools/coverage/test.yml b/...odules/nf-core/samtools/coverage/test.yml → ...dules/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/...modules/nf-core/samtools/flagstat/main.nf → ...odules/cnr-ibba/samtools/flagstat/main.nf b/...modules/nf-core/samtools/flagstat/main.nf → ...odules/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/...nf-core/samtools/flagstat/nextflow.config → ...nr-ibba/samtools/flagstat/nextflow.config b/...nf-core/samtools/flagstat/nextflow.config → ...nr-ibba/samtools/flagstat/nextflow.config
diff --git a/...odules/nf-core/samtools/flagstat/test.yml → ...dules/cnr-ibba/samtools/flagstat/test.yml b/...odules/nf-core/samtools/flagstat/test.yml → ...dules/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/...modules/nf-core/samtools/idxstats/main.nf → ...odules/cnr-ibba/samtools/idxstats/main.nf b/...modules/nf-core/samtools/idxstats/main.nf → ...odules/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/...nf-core/samtools/idxstats/nextflow.config → ...nr-ibba/samtools/idxstats/nextflow.config b/...nf-core/samtools/idxstats/nextflow.config → ...nr-ibba/samtools/idxstats/nextflow.config
diff --git a/...odules/nf-core/samtools/idxstats/test.yml → ...dules/cnr-ibba/samtools/idxstats/test.yml b/...odules/nf-core/samtools/idxstats/test.yml → ...dules/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/nf-core/samtools/stats/main.nf → ...s/modules/cnr-ibba/samtools/stats/main.nf b/tests/modules/nf-core/samtools/stats/main.nf → ...s/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/...es/nf-core/samtools/stats/nextflow.config → ...s/cnr-ibba/samtools/stats/nextflow.config b/...es/nf-core/samtools/stats/nextflow.config → ...s/cnr-ibba/samtools/stats/nextflow.config
diff --git a/tests/modules/cnr-ibba/samtools/stats/test.yml b/tests/modules/cnr-ibba/samtools/stats/test.yml
@@ -0,0 +1,17 @@
+- 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
+  tags:
+    - samtools
+    - samtools/stats
+  files:
+    - path: output/samtools/test.stats
+      md5sum: 045a48208b1c6f5b8af4347fe31f4def
+
+- 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
+  tags:
+    - samtools
+    - samtools/stats
+  files:
+    - path: output/samtools/test.stats
+      md5sum: dfbfa130d4a6925ddd1931dcd8354a43
diff --git a/tests/modules/nf-core/tabix/tabix/main.nf → tests/modules/cnr-ibba/tabix/tabix/main.nf b/tests/modules/nf-core/tabix/tabix/main.nf → 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/...dules/nf-core/tabix/tabix/nextflow.config → ...ules/cnr-ibba/tabix/tabix/nextflow.config b/...dules/nf-core/tabix/tabix/nextflow.config → ...ules/cnr-ibba/tabix/tabix/nextflow.config
diff --git a/tests/modules/cnr-ibba/tabix/tabix/test.yml b/tests/modules/cnr-ibba/tabix/tabix/test.yml
@@ -0,0 +1,32 @@
+- 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
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - 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
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - 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
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.tbi
+      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
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.csi
+      md5sum: 6f733d80ee760fcc8fdbe504a03f2640
diff --git a/tests/modules/nf-core/bcftools/concat/test.yml b/tests/modules/nf-core/bcftools/concat/test.yml
diff --git a/tests/modules/nf-core/samtools/stats/test.yml b/tests/modules/nf-core/samtools/stats/test.yml
diff --git a/tests/modules/nf-core/tabix/tabix/test.yml b/tests/modules/nf-core/tabix/tabix/test.yml
diff --git a/...kflows/nf-core/bam_stats_samtools/main.nf → ...flows/cnr-ibba/bam_stats_samtools/main.nf b/...kflows/nf-core/bam_stats_samtools/main.nf → ...flows/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/...f-core/bam_stats_samtools/nextflow.config → ...r-ibba/bam_stats_samtools/nextflow.config b/...f-core/bam_stats_samtools/nextflow.config → ...r-ibba/bam_stats_samtools/nextflow.config
diff --git a/...flows/nf-core/bam_stats_samtools/test.yml → ...lows/cnr-ibba/bam_stats_samtools/test.yml b/...flows/nf-core/bam_stats_samtools/test.yml → ...lows/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