diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index 508a29ca..e1a4d7b4 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -11,11 +11,11 @@ process GATK4_APPLYBQSR { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index 85c30daf..ff9eb1f9 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -11,11 +11,11 @@ process GATK4_BASERECALIBRATOR { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 064247cc..7c06ccef 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -11,11 +11,11 @@ process GATK4_BEDTOINTERVALLIST { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf index bfe9b8fd..28dd7ccf 100644 --- a/modules/gatk4/calculatecontamination/main.nf +++ b/modules/gatk4/calculatecontamination/main.nf @@ -11,11 +11,11 @@ process GATK4_CALCULATECONTAMINATION { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index 12372bdf..db28e244 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -11,11 +11,11 @@ process GATK4_CREATESEQUENCEDICTIONARY { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf index 66dfda23..b3685171 100644 --- a/modules/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/gatk4/createsomaticpanelofnormals/main.nf @@ -11,11 +11,11 @@ process GATK4_CREATESOMATICPANELOFNORMALS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf index 4cea7086..bfaeedbc 100644 --- a/modules/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/gatk4/estimatelibrarycomplexity/main.nf @@ -11,11 +11,11 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.2.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.2.0--hdfd78af_1" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.2.0--hdfd78af_1" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index ebd081ac..5879618d 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -11,11 +11,11 @@ process GATK4_FASTQTOSAM { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf index 5a784677..b54e07ed 100644 --- a/modules/gatk4/filtermutectcalls/main.nf +++ b/modules/gatk4/filtermutectcalls/main.nf @@ -11,11 +11,11 @@ process GATK4_FILTERMUTECTCALLS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf index 78c6b81f..c5582563 100644 --- a/modules/gatk4/genomicsdbimport/main.nf +++ b/modules/gatk4/genomicsdbimport/main.nf @@ -11,11 +11,11 @@ process GATK4_GENOMICSDBIMPORT { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 09449f12..7919678c 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -11,11 +11,11 @@ process GATK4_GETPILEUPSUMMARIES { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index 4bddbb6d..1e540d17 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -11,11 +11,11 @@ process GATK4_HAPLOTYPECALLER { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index 2f464919..5da651b9 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -11,11 +11,11 @@ process GATK4_INTERVALLISTTOOLS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--hdfd78af_1" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--hdfd78af_1" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf index 0a499def..b8aee764 100644 --- a/modules/gatk4/learnreadorientationmodel/main.nf +++ b/modules/gatk4/learnreadorientationmodel/main.nf @@ -11,11 +11,11 @@ process GATK4_LEARNREADORIENTATIONMODEL { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index b1ff5222..e44f4bfc 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -11,11 +11,11 @@ process GATK4_MARKDUPLICATES { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index 0c9fe5ee..9c5fe26c 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -11,11 +11,11 @@ process GATK4_MERGEBAMALIGNMENT { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index ce9a52c3..28073fcb 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -11,11 +11,11 @@ process GATK4_MERGEVCFS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index 7999eec3..748b1673 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -11,11 +11,11 @@ process GATK4_MUTECT2 { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index b3c9085a..7b5ee696 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -11,11 +11,11 @@ process GATK4_REVERTSAM { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index 324f3bae..843c61ce 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -11,11 +11,11 @@ process GATK4_SAMTOFASTQ { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index 793cc671..01b1d05a 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -11,11 +11,11 @@ process GATK4_SPLITNCIGARREADS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index 28084645..a4e950ae 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -11,11 +11,11 @@ process GATK4_VARIANTFILTRATION { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" + container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { - container "quay.io/biocontainers/gatk4:4.2.0.0--0" + container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml index ed89c6ff..02448b02 100644 --- a/tests/modules/gatk4/applybqsr/test.yml +++ b/tests/modules/gatk4/applybqsr/test.yml @@ -5,7 +5,7 @@ - gatk4 files: - path: output/gatk4/test.bam - md5sum: 87a2eabae2b7b41574f966612b5addae + md5sum: af56f5dd81b95070079d54670507f530 - name: gatk4 applybqsr test_gatk4_applybqsr_intervals command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config @@ -14,7 +14,7 @@ - gatk4 files: - path: output/gatk4/test.bam - md5sum: 9c015d3c1dbd9eee793b7386f432b6aa + md5sum: 0cbfa4be143e988d56ce741b5077510e - name: gatk4 applybqsr test_gatk4_applybqsr_cram command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config @@ -23,4 +23,4 @@ - gatk4 files: - path: output/gatk4/test.bam - md5sum: 02f84815fdbc99c21c8d42ebdcabbbf7 + md5sum: 720ef7453fc3c9def18bbe396062346c diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml index 8736bc32..89d419e0 100644 --- a/tests/modules/gatk4/calculatecontamination/test.yml +++ b/tests/modules/gatk4/calculatecontamination/test.yml @@ -5,7 +5,7 @@ - gatk4 files: - path: output/gatk4/test.contamination.table - md5sum: ff348a26dd09404239a7ed0da7d98874 + md5sum: 5fdcf1728cf98985ce31c038eb24e05c - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config @@ -14,7 +14,7 @@ - gatk4 files: - path: output/gatk4/test.contamination.table - md5sum: ff348a26dd09404239a7ed0da7d98874 + md5sum: 5fdcf1728cf98985ce31c038eb24e05c - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config @@ -23,6 +23,6 @@ - gatk4 files: - path: output/gatk4/test.contamination.table - md5sum: ff348a26dd09404239a7ed0da7d98874 + md5sum: 5fdcf1728cf98985ce31c038eb24e05c - path: output/gatk4/test.segmentation.table - md5sum: 478cb4f69ec001944b9cd0e7e4de01ef + md5sum: 91f28bfe4727a3256810927fc5eba92f diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/test.yml b/tests/modules/gatk4/createsomaticpanelofnormals/test.yml index d3e6c537..d71059ad 100644 --- a/tests/modules/gatk4/createsomaticpanelofnormals/test.yml +++ b/tests/modules/gatk4/createsomaticpanelofnormals/test.yml @@ -6,4 +6,4 @@ files: - path: output/gatk4/test.pon.vcf.gz - path: output/gatk4/test.pon.vcf.gz.tbi - md5sum: d88d2b745c9226ddf284e3494db8b9d2 + md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml index f6597b66..b576075a 100644 --- a/tests/modules/gatk4/fastqtosam/test.yml +++ b/tests/modules/gatk4/fastqtosam/test.yml @@ -5,7 +5,7 @@ - gatk4 files: - path: output/gatk4/test.bam - md5sum: 4967100b2e4912c0e4ce0976d946bafb + md5sum: 0a0d308b219837977b8df9daa26db7de - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config @@ -14,4 +14,4 @@ - gatk4/fastqtosam files: - path: output/gatk4/test.bam - md5sum: 4967100b2e4912c0e4ce0976d946bafb + md5sum: 0a0d308b219837977b8df9daa26db7de diff --git a/tests/modules/gatk4/filtermutectcalls/test.yml b/tests/modules/gatk4/filtermutectcalls/test.yml index b17a306c..d5b97d36 100644 --- a/tests/modules/gatk4/filtermutectcalls/test.yml +++ b/tests/modules/gatk4/filtermutectcalls/test.yml @@ -8,7 +8,7 @@ - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv md5sum: 98e1b87a52999eb8f429ef4a7877eb3f - path: output/gatk4/test.filtered.vcf.gz.tbi - md5sum: d88d2b745c9226ddf284e3494db8b9d2 + md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c tests/config/nextflow.config @@ -20,7 +20,7 @@ - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv md5sum: 98e1b87a52999eb8f429ef4a7877eb3f - path: output/gatk4/test.filtered.vcf.gz.tbi - md5sum: d88d2b745c9226ddf284e3494db8b9d2 + md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c tests/config/nextflow.config @@ -32,4 +32,4 @@ - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv md5sum: 98e1b87a52999eb8f429ef4a7877eb3f - path: output/gatk4/test.filtered.vcf.gz.tbi - md5sum: d88d2b745c9226ddf284e3494db8b9d2 + md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml index 88cca794..6c5e1f84 100644 --- a/tests/modules/gatk4/getpileupsummaries/test.yml +++ b/tests/modules/gatk4/getpileupsummaries/test.yml @@ -5,7 +5,7 @@ - gatk4/getpileupsummaries files: - path: output/gatk4/test.pileups.table - md5sum: 00f92a8f7282d6129f1aca04e2c7d968 + md5sum: 0d19674bef2ff0700d5b02b3463dd210 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config @@ -14,4 +14,4 @@ - gatk4/getpileupsummaries files: - path: output/gatk4/test.pileups.table - md5sum: 00f92a8f7282d6129f1aca04e2c7d968 + md5sum: 0d19674bef2ff0700d5b02b3463dd210 diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml index 66921e45..f4345bc4 100644 --- a/tests/modules/gatk4/markduplicates/test.yml +++ b/tests/modules/gatk4/markduplicates/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.bai md5sum: e9c125e82553209933883b4fe2b8d7c2 - path: output/gatk4/test.bam - md5sum: bda9a7bf5057f2288ed70be3eb8a753f + md5sum: f94271007c1ec8e56adfdd8e45a07bd0 - path: output/gatk4/test.metrics - name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams @@ -17,7 +17,7 @@ - gatk4 files: - path: output/gatk4/test.bai - md5sum: d12be29abba5865b7da0cd23f1a84e86 + md5sum: bad71df9c876e72a5bc0a3e0fd755f92 - path: output/gatk4/test.bam - md5sum: e988925ed850f8d9d966aa6689ae57de + md5sum: e0462bd4fe2cf4beda71e1bd2c66235b - path: output/gatk4/test.metrics diff --git a/tests/modules/gatk4/mergebamalignment/test.yml b/tests/modules/gatk4/mergebamalignment/test.yml index 190a9391..4fb98e3d 100644 --- a/tests/modules/gatk4/mergebamalignment/test.yml +++ b/tests/modules/gatk4/mergebamalignment/test.yml @@ -5,4 +5,4 @@ - gatk4/mergebamalignment files: - path: output/gatk4/test.bam - md5sum: bd4a5e2ea916826aadebb5878333e26f + md5sum: e6f1b343700b7ccb94e81ae127433988 diff --git a/tests/modules/gatk4/mergevcfs/test.yml b/tests/modules/gatk4/mergevcfs/test.yml index 4458f969..884738b0 100644 --- a/tests/modules/gatk4/mergevcfs/test.yml +++ b/tests/modules/gatk4/mergevcfs/test.yml @@ -5,7 +5,7 @@ - gatk4 files: - path: output/gatk4/test.vcf.gz - md5sum: ff48f175e26db2d4b2957762f6d1c715 + md5sum: 5b289bda88d3a3504f2e19ee8cff177c - name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict command: nextflow run tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config @@ -14,4 +14,4 @@ - gatk4 files: - path: output/gatk4/test.vcf.gz - md5sum: ff48f175e26db2d4b2957762f6d1c715 + md5sum: 5b289bda88d3a3504f2e19ee8cff177c diff --git a/tests/modules/gatk4/revertsam/test.yml b/tests/modules/gatk4/revertsam/test.yml index 3f0969c4..c65d3666 100644 --- a/tests/modules/gatk4/revertsam/test.yml +++ b/tests/modules/gatk4/revertsam/test.yml @@ -5,4 +5,4 @@ - gatk4/revertsam files: - path: output/gatk4/test.reverted.bam - md5sum: f778310b18b83b49929eb648594f96dc + md5sum: f783a88deb45c3a2c20ca12cbe1c5652 diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml index d6827db9..146cd329 100644 --- a/tests/modules/gatk4/splitncigarreads/test.yml +++ b/tests/modules/gatk4/splitncigarreads/test.yml @@ -5,4 +5,4 @@ - gatk4/splitncigarreads files: - path: output/gatk4/test.bam - md5sum: 8d05a41f9467e62d3fc1bc725f0869ec + md5sum: bfe6d04a4072f97fdb97dbc502c9d3e2 diff --git a/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml b/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml index 7c9e7ac0..a4478044 100644 --- a/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml +++ b/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml @@ -31,7 +31,7 @@ contains: - "FORMAT=