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Update combine bracken outputs to include meta for publishing purposes
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parent
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commit
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4 changed files with 19 additions and 8 deletions
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@ -330,12 +330,12 @@ process {
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]
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS {
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withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
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ext.prefix = { "kraken2_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/kraken2/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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pattern: '*.txt'
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]
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}
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@ -32,7 +32,7 @@
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},
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"bracken/combinebrackenoutputs": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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@ -1,4 +1,5 @@
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process BRACKEN_COMBINEBRACKENOUTPUTS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
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@ -7,18 +8,18 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
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'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
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input:
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path input
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tuple val(meta), path(input)
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output:
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path "*.txt" , emit: txt
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path "versions.yml", emit: versions
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "bracken_combined.txt"
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def prefix = task.ext.prefix ?: "${meta.id}"
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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def VERSION = '2.7'
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@ -26,7 +27,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
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combine_bracken_outputs.py \\
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$args \\
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--files ${input} \\
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-o ${prefix}
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-o ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -12,12 +12,22 @@ tools:
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licence: ["GPL v3"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input:
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type: file
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description: List of output files from bracken
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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