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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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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.
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@adamrtalbot
adamrtalbot committed Jul 19, 2023
commit 29cf7151cc7a8726e67c2449fbf41653c05b0501
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/access/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_ACCESS {
tag "$meta.id"
label 'process_low'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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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"
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/antitarget/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_ANTITARGET {
tag "$meta.id"
label 'process_low'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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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=0.9.10 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:0.9.10--pyhdfd78af_0' :
'biocontainers/cnvkit:0.9.10--pyhdfd78af_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"
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/call/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_CALL {
tag "$meta.id"
label 'process_single'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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1 change: 1 addition & 0 deletions modules/nf-core/cnvkit/call/meta.yml
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Expand Up @@ -49,3 +49,4 @@ output:

authors:
- "@adamrtalbot"
- "@priesgo"
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/export/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_EXPORT {
tag "$meta.id"
label 'process_single'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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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"
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/genemetrics/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_GENEMETRICS {
tag "$meta.id"
label 'process_low'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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2 changes: 2 additions & 0 deletions modules/nf-core/cnvkit/genemetrics/meta.yml
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Expand Up @@ -42,4 +42,6 @@ output:
pattern: "versions.yml"

authors:
- "@adamrtalbot"
- "@marrip"
- "@priesgo"
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/reference/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_REFERENCE {
tag "$fasta"
label 'process_low'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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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"
2 changes: 1 addition & 1 deletion modules/nf-core/cnvkit/target/main.nf
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Expand Up @@ -2,7 +2,7 @@ process CNVKIT_TARGET {
tag "$meta.id"
label 'process_low'

conda "bioconda::cnvkit=0.9.10 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:0.9.10--pyhdfd78af_0':
'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }"
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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"
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