mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059)
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0 * update md5checksum * commit all files * actually checksum was good, but I suspect something fishy with the tests
This commit is contained in:
Maxime U. Garcia
GitHub
parent
4bd530135f
commit
3b600af50e
34 changed files with 90 additions and 90 deletions
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@ -11,11 +11,11 @@ process GATK4_APPLYBQSR {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_BASERECALIBRATOR {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_BEDTOINTERVALLIST {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_CALCULATECONTAMINATION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_CREATESEQUENCEDICTIONARY {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.2.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.2.0--hdfd78af_1"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.2.0--hdfd78af_1"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_FASTQTOSAM {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_FILTERMUTECTCALLS {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_GENOMICSDBIMPORT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_GETPILEUPSUMMARIES {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_HAPLOTYPECALLER {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_INTERVALLISTTOOLS {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--hdfd78af_1"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--hdfd78af_1"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_LEARNREADORIENTATIONMODEL {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_MARKDUPLICATES {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_MERGEBAMALIGNMENT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_MERGEVCFS {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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@ -11,11 +11,11 @@ process GATK4_MUTECT2 {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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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:
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -6,4 +6,4 @@
|
|||
files:
|
||||
- path: output/gatk4/test.pon.vcf.gz
|
||||
- path: output/gatk4/test.pon.vcf.gz.tbi
|
||||
md5sum: d88d2b745c9226ddf284e3494db8b9d2
|
||||
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- gatk4/mergebamalignment
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: bd4a5e2ea916826aadebb5878333e26f
|
||||
md5sum: e6f1b343700b7ccb94e81ae127433988
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- gatk4/revertsam
|
||||
files:
|
||||
- path: output/gatk4/test.reverted.bam
|
||||
md5sum: f778310b18b83b49929eb648594f96dc
|
||||
md5sum: f783a88deb45c3a2c20ca12cbe1c5652
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- gatk4/splitncigarreads
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 8d05a41f9467e62d3fc1bc725f0869ec
|
||||
md5sum: bfe6d04a4072f97fdb97dbc502c9d3e2
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@
|
|||
contains:
|
||||
- "FORMAT=<ID=AD,Number=R,Type=Integer,Description="
|
||||
- path: output/gatk4/test_panel/vidmap.json
|
||||
md5sum: ee4f6815c433caa8ab101ec45ff328a6
|
||||
md5sum: ac4e96e03bbbc5c72fac77d487e73d9e
|
||||
# gatk4 createsomaticpanelofnormals
|
||||
- path: output/gatk4/test_panel.vcf.gz
|
||||
- path: output/gatk4/test_panel.vcf.gz.tbi
|
||||
|
|
|
|||
Loading…
Reference in a new issue