Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/custom/bwa_idx_mem/main.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process BWA_IDX_MEM {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}bwa${params.fs}0.7.17" : null)
6 conda (params.enable_conda ? "bioconda::bwa=0.7.17 conda-forge::perl" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' :
9 'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }"
10
11 input:
12 tuple val(meta), path(genome), path(reads)
13
14 output:
15 tuple val(meta), path("*.sam"), emit: aligned_sam
16 path "versions.yml" , emit: versions
17
18 when:
19
20
21 script:
22 def args = task.ext.args ?: ''
23 def args2 = task.ext.args2 ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 """
26
27 bwa index $args $genome
28 if [ "${params.fq_single_end}" = "false" ]; then
29 bwa mem \\
30 $args2 \\
31 -t $task.cpus \\
32 -a $genome \\
33 ${reads[0]} > ${prefix}.aligned_1.sam
34 bwa mem \\
35 $args2 \\
36 -t $task.cpus \\
37 -a $genome \\
38 ${reads[1]} > ${prefix}.aligned_2.sam
39 else
40 bwa mem \\
41 $args2 \\
42 -t $task.cpus \\
43 -a $genome \\
44 $reads > ${prefix}.aligned.sam
45
46 fi
47
48 cat <<-END_VERSIONS > versions.yml
49 "${task.process}":
50 bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
51 END_VERSIONS
52 """
53 }