Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/masurca/polish/main.nf @ 15:7c0407ebbdf3
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 17:55:16 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process MASURCA_POLISH { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_micro' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}masurca${params.fs}4.1.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "bioconda::masurca=4.1.0 conda-forge::libgcc-ng" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/masurca:4.1.0--pl5321hb5bd705_1' : |
| kkonganti@11 | 9 'quay.io/biocontainers/masurca:4.1.0--pl5321hb5bd705_1' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(contigs), path(reads) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("${prefix}_contigs.fa"), emit: polished |
| kkonganti@11 | 16 path "versions.yml" , emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 task.ext.when == null || task.ext.when |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 def memory = (task.memory ? task.memory.toGiga() : 16) |
| kkonganti@11 | 24 def mem_per_thread = memory.toGiga().toInteger().div(task.cpus.toInteger()).round(0) |
| kkonganti@11 | 25 def all_reads = "${reads.join(' ')}" |
| kkonganti@11 | 26 prefix = (task.ext.prefix ?: meta.id) |
| kkonganti@11 | 27 """ |
| kkonganti@11 | 28 polca.sh \\ |
| kkonganti@11 | 29 -a $contigs \\ |
| kkonganti@11 | 30 -r '${all_reads}' \\ |
| kkonganti@11 | 31 -t $task.cpus \\ |
| kkonganti@11 | 32 -m $mem_per_thread \\ |
| kkonganti@11 | 33 $args \\ |
| kkonganti@11 | 34 |
| kkonganti@11 | 35 mv 'contigs.fa' "${prefix}.contigs.fa" |
| kkonganti@11 | 36 |
| kkonganti@11 | 37 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 38 "${task.process}": |
| kkonganti@11 | 39 masurca: \$(echo \$(masurca --version 2>&1) | sed 's/^.*version //') |
| kkonganti@11 | 40 END_VERSIONS |
| kkonganti@11 | 41 """ |
| kkonganti@11 | 42 } |