Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/custom/bwa_idx_mem/main.nf @ 12:78a02e8cb092
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:16:59 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process BWA_IDX_MEM { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_micro' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}bwa${params.fs}0.7.17" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "bioconda::bwa=0.7.17 conda-forge::perl" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' : |
| kkonganti@11 | 9 'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(genome), path(reads) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("*.sam"), emit: aligned_sam |
| kkonganti@11 | 16 path "versions.yml" , emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 def args2 = task.ext.args2 ?: '' |
| kkonganti@11 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@11 | 25 """ |
| kkonganti@11 | 26 |
| kkonganti@11 | 27 bwa index $args $genome |
| kkonganti@11 | 28 if [ "${params.fq_single_end}" = "false" ]; then |
| kkonganti@11 | 29 bwa mem \\ |
| kkonganti@11 | 30 $args2 \\ |
| kkonganti@11 | 31 -t $task.cpus \\ |
| kkonganti@11 | 32 -a $genome \\ |
| kkonganti@11 | 33 ${reads[0]} > ${prefix}.aligned_1.sam |
| kkonganti@11 | 34 bwa mem \\ |
| kkonganti@11 | 35 $args2 \\ |
| kkonganti@11 | 36 -t $task.cpus \\ |
| kkonganti@11 | 37 -a $genome \\ |
| kkonganti@11 | 38 ${reads[1]} > ${prefix}.aligned_2.sam |
| kkonganti@11 | 39 else |
| kkonganti@11 | 40 bwa mem \\ |
| kkonganti@11 | 41 $args2 \\ |
| kkonganti@11 | 42 -t $task.cpus \\ |
| kkonganti@11 | 43 -a $genome \\ |
| kkonganti@11 | 44 $reads > ${prefix}.aligned.sam |
| kkonganti@11 | 45 |
| kkonganti@11 | 46 fi |
| kkonganti@11 | 47 |
| kkonganti@11 | 48 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 49 "${task.process}": |
| kkonganti@11 | 50 bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') |
| kkonganti@11 | 51 END_VERSIONS |
| kkonganti@11 | 52 """ |
| kkonganti@11 | 53 } |