process SPADES { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' : 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }" input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) path hmm output: tuple val(meta), path('*.scaffolds.fa.gz') , optional:true, emit: scaffolds tuple val(meta), path('*.contigs.fa.gz') , optional:true, emit: contigs tuple val(meta), path('*.transcripts.fa.gz') , optional:true, emit: transcripts tuple val(meta), path('*.gene_clusters.fa.gz'), optional:true, emit: gene_clusters tuple val(meta), path('*.assembly.gfa.gz') , optional:true, emit: gfa tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def maxmem = task.memory.toGiga() def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : "" def pacbio_reads = pacbio ? "--pacbio $pacbio" : "" def nanopore_reads = nanopore ? "--nanopore $nanopore" : "" def custom_hmms = hmm ? "--custom-hmms $hmm" : "" """ spades.py \\ $args \\ --threads $task.cpus \\ --memory $maxmem \\ $custom_hmms \\ $illumina_reads \\ $pacbio_reads \\ $nanopore_reads \\ -o ./ mv spades.log ${prefix}.spades.log if [ -f scaffolds.fasta ]; then mv scaffolds.fasta ${prefix}.scaffolds.fa gzip -n ${prefix}.scaffolds.fa fi if [ -f contigs.fasta ]; then mv contigs.fasta ${prefix}.contigs.fa gzip -n ${prefix}.contigs.fa fi if [ -f transcripts.fasta ]; then mv transcripts.fasta ${prefix}.transcripts.fa gzip -n ${prefix}.transcripts.fa fi if [ -f assembly_graph_with_scaffolds.gfa ]; then mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa gzip -n ${prefix}.assembly.gfa fi if [ -f gene_clusters.fasta ]; then mv gene_clusters.fasta ${prefix}.gene_clusters.fa gzip -n ${prefix}.gene_clusters.fa fi cat <<-END_VERSIONS > versions.yml "${task.process}": spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//') END_VERSIONS """ }