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CNVKit 0.9.10 update #3651

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merged 10 commits into from
Jul 21, 2023
Merged

CNVKit 0.9.10 update #3651

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b7e667d
upgrade CNVkit to 0.9.10
priesgo Jun 22, 2023
b220ab7
homogenise keywords of all CNVkit modules
priesgo Jun 22, 2023
b7c2f13
Add samtools dependency to bam2seqz module of sequenzautils
JulianMohr Jul 12, 2023
29cf715
Update cnvkit to 0.9.10
adamrtalbot Jul 19, 2023
e5262ab
Merge branch 'master' into cnvkit_0.9.10_updates
adamrtalbot Jul 19, 2023
1bff597
cnvkit 0.9.10 test update
adamrtalbot Jul 19, 2023
88aa48c
update checksums of output files in tests for CNVkit batch
priesgo Jul 21, 2023
66709d9
Merge branch 'master' into cnvkit_0.9.10_updates
priesgo Jul 21, 2023
a77412d
Update cnvkit/export VCF test
adamrtalbot Jul 21, 2023
57d30ea
Additional tags for sequenzautils
adamrtalbot Jul 21, 2023
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6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/access/main.nf
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Expand Up @@ -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)
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1 change: 1 addition & 0 deletions modules/nf-core/cnvkit/access/meta.yml
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Expand Up @@ -55,3 +55,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/antitarget/main.nf
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Expand Up @@ -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)
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2 changes: 2 additions & 0 deletions modules/nf-core/cnvkit/antitarget/meta.yml
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Expand Up @@ -43,4 +43,6 @@ output:
pattern: "versions.yml"

authors:
- "@adamrtalbot"
- "@priesgo"
- "@SusiJo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/batch/main.nf
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Expand Up @@ -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)
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8 changes: 5 additions & 3 deletions modules/nf-core/cnvkit/batch/meta.yml
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Expand Up @@ -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"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/call/main.nf
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Expand Up @@ -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)
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3 changes: 3 additions & 0 deletions modules/nf-core/cnvkit/call/meta.yml
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Expand Up @@ -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:
Expand Down Expand Up @@ -47,3 +49,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/export/main.nf
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Expand Up @@ -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)
Expand Down
1 change: 1 addition & 0 deletions modules/nf-core/cnvkit/export/meta.yml
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Expand Up @@ -43,3 +43,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/genemetrics/main.nf
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Expand Up @@ -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)
Expand Down
6 changes: 5 additions & 1 deletion modules/nf-core/cnvkit/genemetrics/meta.yml
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Expand Up @@ -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: |
Expand Down Expand Up @@ -40,4 +42,6 @@ output:
pattern: "versions.yml"

authors:
- "@adamrtalbot"
- "@marrip"
- "@priesgo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/reference/main.nf
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Expand Up @@ -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
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/cnvkit/reference/meta.yml
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Expand Up @@ -46,4 +46,6 @@ output:
pattern: "versions.yml"

authors:
- "@adamrtalbot"
- "@priesgo"
- "@SusiJo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/target/main.nf
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Expand Up @@ -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)
Expand Down
1 change: 1 addition & 0 deletions modules/nf-core/cnvkit/target/meta.yml
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Expand Up @@ -58,3 +58,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
2 changes: 1 addition & 1 deletion modules/nf-core/sequenzautils/bam2seqz/main.nf
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Expand Up @@ -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' }"
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/sequenzautils/bam2seqz/meta.yml
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@@ -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:
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/sequenzautils/gcwiggle/meta.yml
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@@ -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:
Expand Down
14 changes: 7 additions & 7 deletions tests/modules/nf-core/cnvkit/batch/test.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
5 changes: 3 additions & 2 deletions tests/modules/nf-core/cnvkit/export/test.yml
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Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions tests/modules/nf-core/cnvkit/genemetrics/test.yml
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Expand Up @@ -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
Expand All @@ -18,4 +18,4 @@
- path: "output/cnvkit/test.tsv"
md5sum: 622e154a107301da6f456b4b3196b79d
- path: "output/cnvkit/versions.yml"
md5sum: dbc07d4b63731d5077845f9b53226260
md5sum: 31293c53d7c9ef99bad1dc5b80929ee8
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