mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
70 lines
2.5 KiB
Text
70 lines
2.5 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } 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), publish_id:meta.id) }
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::spades=3.15.0" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(reads)
|
||
|
|
path hmm
|
||
|
|
val coronaspades
|
||
|
|
|
||
|
|
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 '*.version.txt' , 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" : ""
|
||
|
|
def command = coronaspades ? "coronaspades.py" : "spades.py"
|
||
|
|
"""
|
||
|
|
$command \\
|
||
|
|
$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
|
||
|
|
|
||
|
|
echo \$(spades.py --version 2>&1) | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|