mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
69 lines
2.5 KiB
Text
69 lines
2.5 KiB
Text
// 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: versions
|
|
|
|
script:
|
|
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
|
|
"""
|
|
}
|