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comparison 0.5.0/modules/bwa/mem/main.nf @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 process BWA_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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--he4a0461_11' :
9 'quay.io/biocontainers/bwa:0.7.17--he4a0461_11' }"
10
11 input:
12 tuple val(meta), path(reads), path(index)
13 val index2
14
15 output:
16 tuple val(meta), path("*.sam"), emit: aligned_sam
17 path "versions.yml" , emit: versions
18
19 when:
20
21
22 script:
23 def args = task.ext.args ?: ''
24 def args2 = task.ext.args2 ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}"
26 def this_index = (index ?: index2)
27 """
28
29 if [ "${params.fq_single_end}" = "false" ]; then
30 bwa mem \\
31 $args \\
32 -t $task.cpus \\
33 $this_index \\
34 ${reads[0]} ${reads[1]} > ${prefix}.aligned.sam
35 else
36 bwa mem \\
37 $args \\
38 -t $task.cpus \\
39 -a \\
40 $this_index \\
41 $reads > ${prefix}.aligned.sam
42
43 fi
44
45 cat <<-END_VERSIONS > versions.yml
46 "${task.process}":
47 bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
48 END_VERSIONS
49 """
50 }