nf-core_modules/modules/spades/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SPADES {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0"
} else {
container "quay.io/biocontainers/spades:3.15.3--h95f258a_0"
}
input:
tuple val(meta), path(reads)
path hmm
output:
tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
tuple val(meta), path('*.contigs.fa') , optional:true, emit: contigs
tuple val(meta), path('*.transcripts.fa') , optional:true, emit: transcripts
tuple val(meta), path('*.gene_clusters.fa'), optional:true, emit: gene_clusters
tuple val(meta), path('*.assembly.gfa') , optional:true, emit: gfa
tuple val(meta), path('*.log') , emit: log
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
"""
spades.py \\
$options.args \\
--threads $task.cpus \\
$custom_hmms \\
$input_reads \\
-o ./
mv spades.log ${prefix}.spades.log
if [ -f scaffolds.fasta ]; then
mv scaffolds.fasta ${prefix}.scaffolds.fa
fi
if [ -f contigs.fasta ]; then
mv contigs.fasta ${prefix}.contigs.fa
fi
if [ -f transcripts.fasta ]; then
mv transcripts.fasta ${prefix}.transcripts.fa
fi
if [ -f assembly_graph_with_scaffolds.gfa ]; then
mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa
fi
if [ -f gene_clusters.fasta ]; then
mv gene_clusters.fasta ${prefix}.gene_clusters.fa
fi
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
END_VERSIONS
"""
}