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e7845e2472
* msisensor2: Add msisensor2 module * msisensor2/scan module added * msisensor2 tests added Changes: - tests added for msisensor2 from the msisensor2 github repo. No available tests from NF-Core test repo. Relates to #1976 * msisensor2 slight bump in stuff * msisensor2: Replaced spelling of 'tumour' with 'tumor' * msisensor2: fix linting, testing and containers Relates to #1976 Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
48 lines
1.7 KiB
Text
48 lines
1.7 KiB
Text
process MSISENSOR2_MSI {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0':
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'quay.io/biocontainers/msisensor2:0.1--hd03093a_0' }"
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input:
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tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals)
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path scan
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path(models, stageAs: "models/*")
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output:
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tuple val(meta), path("${prefix}") , emit: msi
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tuple val(meta), path("${prefix}_dis") , emit: distribution
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tuple val(meta), path("${prefix}_somatic"), emit: somatic
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def scan_cmd = scan ? "-d $scan" : ""
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def model_cmd = models ? "-M models/" : ""
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def tumor_bam_cmd = tumor_bam ? "-t $tumor_bam" : ""
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def normal_bam_cmd = normal_bam ? "-n $normal_bam" : ""
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def interval_command = intervals ? "-e $intervals" : ""
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"""
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msisensor2 msi \\
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-b ${task.cpus} \\
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$args \\
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$model_cmd \\
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$scan_cmd \\
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$interval_command \\
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$tumor_bam_cmd \\
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$normal_bam_cmd \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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msisensor2: \$(echo \$(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
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END_VERSIONS
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"""
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}
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