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661bdb645e
* Change spades module * correct meta map description * adjust memory handling * remove trailing whitespace * fix hmm input * Update modules/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
80 lines
3 KiB
Text
80 lines
3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::spades=3.15.3' : 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:3.15.3--h95f258a_0"
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} else {
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container "quay.io/biocontainers/spades:3.15.3--h95f258a_0"
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}
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input:
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tuple val(meta), path(illumina), path(pacbio), path(nanopore)
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path hmm
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output:
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tuple val(meta), path('*.scaffolds.fa.gz') , optional:true, emit: scaffolds
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tuple val(meta), path('*.contigs.fa.gz') , optional:true, emit: contigs
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tuple val(meta), path('*.transcripts.fa.gz') , optional:true, emit: transcripts
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tuple val(meta), path('*.gene_clusters.fa.gz'), optional:true, emit: gene_clusters
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tuple val(meta), path('*.assembly.gfa.gz') , optional:true, emit: gfa
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def maxmem = task.memory.toGiga()
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def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
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def pacbio_reads = pacbio ? "--pacbio $pacbio" : ""
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def nanopore_reads = nanopore ? "--nanopore $nanopore" : ""
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def custom_hmms = hmm ? "--custom-hmms $hmm" : ""
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"""
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spades.py \\
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$options.args \\
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--threads $task.cpus \\
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--memory $maxmem \\
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$custom_hmms \\
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$illumina_reads \\
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$pacbio_reads \\
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$nanopore_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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gzip -n ${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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gzip -n ${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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gzip -n ${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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gzip -n ${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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gzip -n ${prefix}.gene_clusters.fa
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fi
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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