Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/modules/bwa/mem/main.nf @ 0:97cd2f532efe
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process BWA_MEM { |
| kkonganti@0 | 2 tag "$meta.id" |
| kkonganti@0 | 3 label 'process_micro' |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}bwa${params.fs}0.7.17" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? "bioconda::bwa=0.7.17 conda-forge::perl" : null) |
| kkonganti@0 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@0 | 8 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' : |
| kkonganti@0 | 9 'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }" |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 input: |
| kkonganti@0 | 12 tuple val(meta), path(reads), path(index) |
| kkonganti@0 | 13 val index2 |
| kkonganti@0 | 14 |
| kkonganti@0 | 15 output: |
| kkonganti@0 | 16 tuple val(meta), path("*.sam"), emit: aligned_sam |
| kkonganti@0 | 17 path "versions.yml" , emit: versions |
| kkonganti@0 | 18 |
| kkonganti@0 | 19 when: |
| kkonganti@0 | 20 |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 script: |
| kkonganti@0 | 23 def args = task.ext.args ?: '' |
| kkonganti@0 | 24 def args2 = task.ext.args2 ?: '' |
| kkonganti@0 | 25 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@0 | 26 def this_index = (index ?: index2) |
| kkonganti@0 | 27 """ |
| kkonganti@0 | 28 |
| kkonganti@0 | 29 if [ "${params.fq_single_end}" = "false" ]; then |
| kkonganti@0 | 30 bwa mem \\ |
| kkonganti@0 | 31 $args \\ |
| kkonganti@0 | 32 -t $task.cpus \\ |
| kkonganti@0 | 33 $this_index \\ |
| kkonganti@0 | 34 ${reads[0]} ${reads[1]} > ${prefix}.aligned.sam |
| kkonganti@0 | 35 else |
| kkonganti@0 | 36 bwa mem \\ |
| kkonganti@0 | 37 $args \\ |
| kkonganti@0 | 38 -t $task.cpus \\ |
| kkonganti@0 | 39 -a \\ |
| kkonganti@0 | 40 $this_index \\ |
| kkonganti@0 | 41 $reads > ${prefix}.aligned.sam |
| kkonganti@0 | 42 |
| kkonganti@0 | 43 fi |
| kkonganti@0 | 44 |
| kkonganti@0 | 45 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 46 "${task.process}": |
| kkonganti@0 | 47 bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') |
| kkonganti@0 | 48 END_VERSIONS |
| kkonganti@0 | 49 """ |
| kkonganti@0 | 50 } |