diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf index fd102f67..aff83c9f 100644 --- a/modules/picard/addorreplacereadgroups/main.nf +++ b/modules/picard/addorreplacereadgroups/main.nf @@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf index 62989565..0042c3f1 100644 --- a/modules/picard/cleansam/main.nf +++ b/modules/picard/cleansam/main.nf @@ -2,10 +2,10 @@ process PICARD_CLEANSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf index 06b6b8f3..52d5c84a 100644 --- a/modules/picard/collecthsmetrics/main.nf +++ b/modules/picard/collecthsmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index 3c3152df..6fe9881b 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index cab1fe0c..e231afe2 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf index 2348c496..16a5ff19 100644 --- a/modules/picard/createsequencedictionary/main.nf +++ b/modules/picard/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/picard/crosscheckfingerprints/main.nf b/modules/picard/crosscheckfingerprints/main.nf index d3b59402..c7c4766c 100644 --- a/modules/picard/crosscheckfingerprints/main.nf +++ b/modules/picard/crosscheckfingerprints/main.nf @@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(input1) diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index adedcdc2..e17c4686 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf index 539b1082..616acce8 100644 --- a/modules/picard/fixmateinformation/main.nf +++ b/modules/picard/fixmateinformation/main.nf @@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf index c92abfeb..a82f1466 100644 --- a/modules/picard/liftovervcf/main.nf +++ b/modules/picard/liftovervcf/main.nf @@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index 1565c647..87f913d4 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index 1e32c63a..d65f518c 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index cee60fd1..5e09d907 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -2,10 +2,10 @@ process PICARD_SORTSAM { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf index fb8dbb79..8f886393 100644 --- a/modules/picard/sortvcf/main.nf +++ b/modules/picard/sortvcf/main.nf @@ -2,10 +2,10 @@ process PICARD_SORTVCF { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.1" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(vcf)