Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/bbtools/bbmerge/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 process BBTOOLS_BBMERGE { |
| kkonganti@1 | 2 tag "$meta.id" |
| kkonganti@1 | 3 label 'process_micro' |
| kkonganti@1 | 4 |
| kkonganti@1 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}bbtools${params.fs}38.94" : null) |
| kkonganti@1 | 6 conda (params.enable_conda ? "conda-forge::pbzip2 bioconda::bbmap=38.95" : null) |
| kkonganti@1 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@1 | 8 'https://depot.galaxyproject.org/singularity/bbmap:38.95--he522d1c_0' : |
| kkonganti@1 | 9 'quay.io/biocontainers/bbmap:38.95--he522d1c_0' }" |
| kkonganti@1 | 10 |
| kkonganti@1 | 11 input: |
| kkonganti@1 | 12 tuple val(meta), path(reads) |
| kkonganti@1 | 13 |
| kkonganti@1 | 14 output: |
| kkonganti@1 | 15 tuple val(meta), path("*.fastq.gz"), emit: fastq |
| kkonganti@1 | 16 tuple val(meta), path("*.log") , emit: log |
| kkonganti@1 | 17 path "versions.yml" , emit: versions |
| kkonganti@1 | 18 |
| kkonganti@1 | 19 when: |
| kkonganti@1 | 20 !meta.single_end |
| kkonganti@1 | 21 |
| kkonganti@1 | 22 script: |
| kkonganti@1 | 23 def args = task.ext.args ?: '' |
| kkonganti@1 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@1 | 25 def in_files = "in1=${reads[0]} in2=${reads[1]}" |
| kkonganti@1 | 26 def out_file = "out=${prefix}.bbmerge.fastq.gz" |
| kkonganti@1 | 27 def adapters_file = file (meta.adapters) |
| kkonganti@1 | 28 def adapters = !("${adapters_file.simpleName}" ==~ 'dummy_file.*') && adapters_file.exits() ? "adapters=${meta.adapters}" : '' |
| kkonganti@1 | 29 def args_formatted = args.replaceAll('=\s+', '=') |
| kkonganti@1 | 30 """ |
| kkonganti@1 | 31 bbmerge.sh \\ |
| kkonganti@1 | 32 -Xmx${task.memory.toGiga()}G \\ |
| kkonganti@1 | 33 threads=$task.cpus \\ |
| kkonganti@1 | 34 $args_formatted \\ |
| kkonganti@1 | 35 $adapters \\ |
| kkonganti@1 | 36 $in_files \\ |
| kkonganti@1 | 37 $out_file &> ${prefix}.bbmerge.log |
| kkonganti@1 | 38 |
| kkonganti@1 | 39 cat <<-END_VERSIONS > versions.yml |
| kkonganti@1 | 40 "${task.process}": |
| kkonganti@1 | 41 bbmerge: \$( bbversion.sh ) |
| kkonganti@1 | 42 END_VERSIONS |
| kkonganti@1 | 43 """ |
| kkonganti@1 | 44 } |