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57 lines
2.9 KiB
Plaintext
57 lines
2.9 KiB
Plaintext
process MERQURYFK_MERQURYFK {
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tag "$meta.id"
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label 'process_medium'
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if (params.enable_conda) {
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error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
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}
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
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input:
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tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly)
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output:
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tuple val(meta), path("${prefix}.completeness.stats") , emit: stats
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tuple val(meta), path("${prefix}.*_only.bed") , emit: bed
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tuple val(meta), path("${prefix}.*.qv") , emit: assembly_qv
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tuple val(meta), path("${prefix}.*.spectra-cn.fl.png"), emit: spectra_cn_fl_png, optional: true
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tuple val(meta), path("${prefix}.*.spectra-cn.fl.pdf"), emit: spectra_cn_fl_pdf, optional: true
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tuple val(meta), path("${prefix}.*.spectra-cn.ln.png"), emit: spectra_cn_ln_png, optional: true
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tuple val(meta), path("${prefix}.*.spectra-cn.ln.pdf"), emit: spectra_cn_ln_pdf, optional: true
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tuple val(meta), path("${prefix}.*.spectra-cn.st.png"), emit: spectra_cn_st_png, optional: true
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tuple val(meta), path("${prefix}.*.spectra-cn.st.pdf"), emit: spectra_cn_st_pdf, optional: true
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tuple val(meta), path("${prefix}.qv") , emit: qv
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tuple val(meta), path("${prefix}.spectra-asm.fl.png") , emit: spectra_asm_fl_png, optional: true
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tuple val(meta), path("${prefix}.spectra-asm.fl.pdf") , emit: spectra_asm_fl_pdf, optional: true
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tuple val(meta), path("${prefix}.spectra-asm.ln.png") , emit: spectra_asm_ln_png, optional: true
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tuple val(meta), path("${prefix}.spectra-asm.ln.pdf") , emit: spectra_asm_ln_pdf, optional: true
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tuple val(meta), path("${prefix}.spectra-asm.st.png") , emit: spectra_asm_st_png, optional: true
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tuple val(meta), path("${prefix}.spectra-asm.st.pdf") , emit: spectra_asm_st_pdf, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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MerquryFK \\
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$args \\
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-T$task.cpus \\
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${fastk_ktab.find{ it.toString().endsWith(".ktab") }} \\
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$assembly \\
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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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