CNVKit 0.9.10 update (nf-core#3651)

* upgrade CNVkit to 0.9.10 * homogenise keywords of all CNVkit modules * Add samtools dependency to bam2seqz module of sequenzautils Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests) * Update cnvkit to 0.9.10 Changes: - Update cnvkit to 0.9.10 - Update samtools in cnvkit modules to 1.17 Based on nf-core#3545 authored by @priesgo. * cnvkit 0.9.10 test update * update checksums of output files in tests for CNVkit batch * Update cnvkit/export VCF test * Additional tags for sequenzautils --------- Co-authored-by: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com> Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com>
limrp · Jul 28, 2023 · 35a1d9d · 35a1d9d
1 parent fb4126c
commit 35a1d9d
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Showing 22 changed files with 61 additions and 40 deletions.
diff --git a/modules/nf-core/cnvkit/access/main.nf b/modules/nf-core/cnvkit/access/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_ACCESS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/cnvkit/access/meta.yml b/modules/nf-core/cnvkit/access/meta.yml
@@ -55,3 +55,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_ANTITARGET {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(targets)

diff --git a/modules/nf-core/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml
@@ -43,4 +43,6 @@ output:
       pattern: "versions.yml"
 
 authors:
+  - "@adamrtalbot"
+  - "@priesgo"
   - "@SusiJo"
diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_BATCH {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' :
-        'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' :
+        'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }"
 
     input:
     tuple val(meta), path(tumor), path(normal)

diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml
@@ -77,10 +77,12 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
 authors:
-  - "@kaurravneet4123"
-  - "@KevinMenden"
-  - "@MaxUlysse"
+  - "@adamrtalbot"
   - "@drpatelh"
   - "@fbdtemme"
+  - "@kaurravneet4123"
+  - "@KevinMenden"
   - "@lassefolkersen"
+  - "@MaxUlysse"
+  - "@priesgo"
   - "@SusiJo"
diff --git a/modules/nf-core/cnvkit/call/main.nf b/modules/nf-core/cnvkit/call/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_CALL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(cns), path(vcf)

diff --git a/modules/nf-core/cnvkit/call/meta.yml b/modules/nf-core/cnvkit/call/meta.yml
@@ -2,6 +2,8 @@ name: cnvkit_call
 description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number
 keywords:
   - cnvkit
+  - bam
+  - fasta
   - copy number
 tools:
   - cnvkit:
@@ -47,3 +49,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/export/main.nf b/modules/nf-core/cnvkit/export/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_EXPORT {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(cns)

diff --git a/modules/nf-core/cnvkit/export/meta.yml b/modules/nf-core/cnvkit/export/meta.yml
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_GENEMETRICS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(cnr), path(cns)

diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml
@@ -2,7 +2,9 @@ name: cnvkit_genemetrics
 description: Copy number variant detection from high-throughput sequencing data
 keywords:
   - cnvkit
-  - genemetrics
+  - bam
+  - fasta
+  - copy number
 tools:
   - cnvkit:
       description: |
@@ -40,4 +42,6 @@ output:
       pattern: "versions.yml"
 
 authors:
+  - "@adamrtalbot"
   - "@marrip"
+  - "@priesgo"
diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_REFERENCE {
     tag "$fasta"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     path fasta

diff --git a/modules/nf-core/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml
@@ -46,4 +46,6 @@ output:
       pattern: "versions.yml"
 
 authors:
+  - "@adamrtalbot"
+  - "@priesgo"
   - "@SusiJo"
diff --git a/modules/nf-core/cnvkit/target/main.nf b/modules/nf-core/cnvkit/target/main.nf
@@ -2,10 +2,10 @@ process CNVKIT_TARGET {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
-        'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0':
+        'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(baits)

diff --git a/modules/nf-core/cnvkit/target/meta.yml b/modules/nf-core/cnvkit/target/meta.yml
@@ -58,3 +58,4 @@ output:
 
 authors:
   - "@adamrtalbot"
+  - "@priesgo"
diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf
@@ -2,7 +2,7 @@ process SEQUENZAUTILS_BAM2SEQZ {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::sequenza-utils=3.0.0"
+    conda "bioconda::samtools=1.15.1 bioconda::sequenza-utils=3.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' :
         'biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }"

diff --git a/modules/nf-core/sequenzautils/bam2seqz/meta.yml b/modules/nf-core/sequenzautils/bam2seqz/meta.yml
@@ -1,6 +1,8 @@
 name: sequenzautils_bam2seqz
 description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
 keywords:
+  - sequenzautils
+  - copy number
   - bam2seqz
 tools:
   - sequenzautils:

diff --git a/modules/nf-core/sequenzautils/gcwiggle/meta.yml b/modules/nf-core/sequenzautils/gcwiggle/meta.yml
@@ -1,6 +1,8 @@
 name: sequenzautils_gcwiggle
 description: Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size.
 keywords:
+  - sequenzautils
+  - copy number
   - gc_wiggle
 tools:
   - sequenzautils:

diff --git a/tests/modules/nf-core/cnvkit/batch/test.yml b/tests/modules/nf-core/cnvkit/batch/test.yml
@@ -12,7 +12,7 @@
     - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
       md5sum: 203caf8cef6935bb50b4138097955cb8
     - path: output/cnvkit/test.paired_end.sorted.bintest.cns
-      md5sum: 6544d979475def8a9f69ba42a985668d
+      md5sum: b6701cceb525c3087f4dad432d20100c
     - path: output/cnvkit/test.paired_end.sorted.call.cns
       md5sum: f2ca59b4d50b0c317adc526c1b99b622
     - path: output/cnvkit/test.paired_end.sorted.cnr
@@ -46,7 +46,7 @@
     - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
       md5sum: 203caf8cef6935bb50b4138097955cb8
     - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
-      md5sum: 6544d979475def8a9f69ba42a985668d
+      md5sum: b6701cceb525c3087f4dad432d20100c
     - path: output/cnvkit/test2.paired_end.sorted.call.cns
       md5sum: f6de754c34f780e6befee5b3ff0893f8
     - path: output/cnvkit/test2.paired_end.sorted.cnr
@@ -76,7 +76,7 @@
     - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
       md5sum: 203caf8cef6935bb50b4138097955cb8
     - path: output/cnvkit/test2.paired_end.sorted.bintest.cns
-      md5sum: 6544d979475def8a9f69ba42a985668d
+      md5sum: b6701cceb525c3087f4dad432d20100c
     - path: output/cnvkit/test2.paired_end.sorted.call.cns
       md5sum: f6de754c34f780e6befee5b3ff0893f8
     - path: output/cnvkit/test2.paired_end.sorted.cnr
@@ -99,7 +99,7 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
       md5sum: 067115082c4af4b64d58c0dc3a3642e4
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+      md5sum: 7a66b5f63acb05e6dfb0784c215851ec
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
       md5sum: f7caeca04aba28b125ce26b511f42afb
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
@@ -122,7 +122,7 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
       md5sum: 067115082c4af4b64d58c0dc3a3642e4
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+      md5sum: 7a66b5f63acb05e6dfb0784c215851ec
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
       md5sum: f7caeca04aba28b125ce26b511f42afb
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
@@ -147,7 +147,7 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
       md5sum: 067115082c4af4b64d58c0dc3a3642e4
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: 68b62b75cd91b2ffe5633686fb943490
+      md5sum: 97ccb82da921185fcb033027914edf40
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
       md5sum: df196edd72613c59186f4d87df3dc4a4
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
@@ -172,7 +172,7 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
       md5sum: 067115082c4af4b64d58c0dc3a3642e4
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-      md5sum: 68b62b75cd91b2ffe5633686fb943490
+      md5sum: 97ccb82da921185fcb033027914edf40
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
       md5sum: df196edd72613c59186f4d87df3dc4a4
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr

diff --git a/tests/modules/nf-core/cnvkit/export/test.yml b/tests/modules/nf-core/cnvkit/export/test.yml
@@ -17,8 +17,9 @@
     - path: output/cnvkit/test.vcf
       contains:
         - "##fileformat=VCFv4.2"
-        - "##source=CNVkit v0.9.9"
-        - "chr1\t160786623\t.\tN\t<DEL>\t.\t.\tIMPRECISE;SVTYPE=DEL;END=160786747;SVLEN=-124;FOLD_CHANGE=0.271780;FOLD_CHANGE_LOG=-1.879490;PROBES=1\tGT:GQ\t0/1:1"
+        - "##source=CNVkit v0.9.10"
+
+        - "chr1\t160786623\t.\tN\t<DEL>\t.\t.\tIMPRECISE;SVTYPE=DEL;END=160786747;SVLEN=-124;FOLD_CHANGE=0.2717797741778673;FOLD_CHANGE_LOG=-1.87949;PROBES=1\tGT:GQ\t0/1:1"
     - path: output/cnvkit/versions.yml
 
 - name: cnvkit export test_cnvkit_export_cdt

diff --git a/tests/modules/nf-core/cnvkit/genemetrics/test.yml b/tests/modules/nf-core/cnvkit/genemetrics/test.yml
@@ -7,7 +7,7 @@
     - path: "output/cnvkit/test.tsv"
       md5sum: 2a18eca552ea33faab1d39795d9e051c
     - path: "output/cnvkit/versions.yml"
-      md5sum: 3d211e0077f86038ae454bdce8262cea
+      md5sum: 3158be0ead57ad4397444cdbe786994a
 
 - name: cnvkit genemetrics without cns
   command: nextflow run ./tests/modules/nf-core/cnvkit/genemetrics -entry test_cnvkit_genemetrics_without_cns -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/genemetrics/nextflow.config
@@ -18,4 +18,4 @@
     - path: "output/cnvkit/test.tsv"
       md5sum: 622e154a107301da6f456b4b3196b79d
     - path: "output/cnvkit/versions.yml"
-      md5sum: dbc07d4b63731d5077845f9b53226260
+      md5sum: 31293c53d7c9ef99bad1dc5b80929ee8