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Merge pull request #1707 from matthdsm/bump/picard

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bump picard versions
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Matthias De Smet 2022-06-03 06:39:19 +02:00 committed by GitHub
commit 24403ce45d
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GPG key ID: 4AEE18F83AFDEB23
14 changed files with 42 additions and 42 deletions
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6
modules/picard/addorreplacereadgroups/main.nf
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@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/cleansam/main.nf
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@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/collecthsmetrics/main.nf
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@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/collectmultiplemetrics/main.nf
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@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/createsequencedictionary/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

6
modules/picard/crosscheckfingerprints/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(input1) tuple val(meta), path(input1)

6
modules/picard/filtersamreads/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(readlist) tuple val(meta), path(bam), path(readlist)

6
modules/picard/fixmateinformation/main.nf
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@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/liftovervcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(input_vcf) tuple val(meta), path(input_vcf)

6
modules/picard/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/mergesamfiles/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bams) tuple val(meta), path(bams)

6
modules/picard/sortsam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTSAM {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/sortvcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTVCF {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)