Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/spades/assemble/main.nf @ 11:a5f31c44f8c9
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:11:44 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process SPADES_ASSEMBLE { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_higher' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' : |
| kkonganti@11 | 9 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(illumina), path(pacbio), path(nanopore) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 path "${meta.id}${params.fs}*" |
| kkonganti@11 | 16 tuple val(meta), path("${meta.id}${params.fs}scaffolds.fasta"), emit: assembly, optional: true |
| kkonganti@11 | 17 tuple val(meta), path("${meta.id}${params.fs}spades.log") , emit: log |
| kkonganti@11 | 18 path "versions.yml" , emit: versions |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 when: |
| kkonganti@11 | 21 task.ext.when == null || task.ext.when |
| kkonganti@11 | 22 |
| kkonganti@11 | 23 script: |
| kkonganti@11 | 24 def args = task.ext.args ?: '' |
| kkonganti@11 | 25 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@11 | 26 def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : "" |
| kkonganti@11 | 27 def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : "" |
| kkonganti@11 | 28 def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : "" |
| kkonganti@11 | 29 def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : "" |
| kkonganti@11 | 30 def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : "" |
| kkonganti@11 | 31 """ |
| kkonganti@11 | 32 spades.py \\ |
| kkonganti@11 | 33 $args \\ |
| kkonganti@11 | 34 --threads $task.cpus \\ |
| kkonganti@11 | 35 $maxmem \\ |
| kkonganti@11 | 36 $custom_hmms \\ |
| kkonganti@11 | 37 $illumina_reads \\ |
| kkonganti@11 | 38 $pacbio_reads \\ |
| kkonganti@11 | 39 $nanopore_reads \\ |
| kkonganti@11 | 40 --tmp-dir ${prefix}${params.fs}tmp |
| kkonganti@11 | 41 -o ${prefix} |
| kkonganti@11 | 42 |
| kkonganti@11 | 43 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 44 "${task.process}": |
| kkonganti@11 | 45 spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//') |
| kkonganti@11 | 46 END_VERSIONS |
| kkonganti@11 | 47 """ |
| kkonganti@11 | 48 } |