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CNVKit 0.9.10 update (#3651)
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* 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 #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 <[email protected]>
Co-authored-by: Julian Mohr <[email protected]>
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3 people authored Jul 21, 2023
1 parent 1038d3d commit 3b63e1d
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Showing 22 changed files with 61 additions and 40 deletions.
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/access/main.nf
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
Expand Up @@ -55,3 +55,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/antitarget/main.nf
Original file line number Diff line number Diff line change
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)
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/cnvkit/antitarget/meta.yml
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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)
Expand Down
3 changes: 3 additions & 0 deletions modules/nf-core/cnvkit/call/meta.yml
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
Expand Up @@ -43,3 +43,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
6 changes: 3 additions & 3 deletions modules/nf-core/cnvkit/genemetrics/main.nf
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
Expand Up @@ -58,3 +58,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
2 changes: 1 addition & 1 deletion modules/nf-core/sequenzautils/bam2seqz/main.nf
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
@@ -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
Original file line number Diff line number Diff line change
@@ -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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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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