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70 lines
2.5 KiB
Text
70 lines
2.5 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SPADES {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::spades=3.15.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
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} else {
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container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
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}
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input:
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tuple val(meta), path(reads)
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path hmm
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val coronaspades
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output:
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tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
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tuple val(meta), path('*.contigs.fa') , optional:true, emit: contigs
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tuple val(meta), path('*.transcripts.fa') , optional:true, emit: transcripts
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tuple val(meta), path('*.gene_clusters.fa'), optional:true, emit: gene_clusters
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tuple val(meta), path('*.assembly.gfa') , optional:true, emit: gfa
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tuple val(meta), path('*.log') , emit: log
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path '*.version.txt' , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
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def command = coronaspades ? "coronaspades.py" : "spades.py"
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"""
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$command \\
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$options.args \\
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--threads $task.cpus \\
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$custom_hmms \\
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$input_reads \\
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-o ./
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mv spades.log ${prefix}.spades.log
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if [ -f scaffolds.fasta ]; then
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mv scaffolds.fasta ${prefix}.scaffolds.fa
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fi
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if [ -f contigs.fasta ]; then
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mv contigs.fasta ${prefix}.contigs.fa
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fi
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if [ -f transcripts.fasta ]; then
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mv transcripts.fasta ${prefix}.transcripts.fa
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fi
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if [ -f assembly_graph_with_scaffolds.gfa ]; then
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mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa
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fi
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if [ -f gene_clusters.fasta ]; then
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mv gene_clusters.fasta ${prefix}.gene_clusters.fa
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fi
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echo \$(spades.py --version 2>&1) | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//' > ${software}.version.txt
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"""
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}
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