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45 lines
1.6 KiB
Text
45 lines
1.6 KiB
Text
process MERQURYFK_KATCOMP {
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tag "$meta.id"
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label 'process_medium'
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if (params.enable_conda) {
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error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
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}
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container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
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input:
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tuple val(meta), path(fastk1_hist), path(fastk1_ktab), path(fastk2_hist), path(fastk2_ktab)
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output:
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tuple val(meta), path("*.fi.png"), emit: filled_png , optional: true
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tuple val(meta), path("*.ln.png"), emit: line_png , optional: true
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tuple val(meta), path("*.st.png"), emit: stacked_png, optional: true
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tuple val(meta), path("*.fi.pdf"), emit: filled_pdf , optional: true
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tuple val(meta), path("*.ln.pdf"), emit: line_pdf , optional: true
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tuple val(meta), path("*.st.pdf"), emit: stacked_pdf, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
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def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494'
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"""
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KatComp \\
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$args \\
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-T$task.cpus \\
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${fastk1_ktab.find{ it.toString().endsWith(".ktab") }} \\
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${fastk2_ktab.find{ it.toString().endsWith(".ktab") }} \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastk: $FASTK_VERSION
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merquryfk: $MERQURY_VERSION
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r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
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END_VERSIONS
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"""
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}
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