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comparison 0.6.1/modules/kma/align/main.nf @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
1 process KMA_ALIGN {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}kma${params.fs}1.4.4" : null)
6 conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
9 'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
10
11 input:
12 tuple val(meta), path(reads), path(index)
13
14 output:
15 path "${meta.id}_kma_res"
16 tuple val(meta), path("${meta.id}_kma_res${params.fs}*.res") , emit: res
17 tuple val(meta), path("${meta.id}_kma_res${params.fs}*.mapstat") , emit: mapstat, optional: true
18 tuple val(meta), path("${meta.id}_kma_res${params.fs}*.frag.gz") , emit: frags, optional: true
19 tuple val(meta), path("${meta.id}_kma_res${params.fs}*_template_hits.txt"), emit: hits, optional: true
20 path "versions.yml" , emit: versions
21
22 when:
23 task.ext.when == null || task.ext.when
24
25 script:
26 def args = task.ext.args ?: ''
27 def prefix = task.ext.prefix ?: "${meta.id}"
28 def reads_in = (meta.single_end ? "-i $reads" : "-ipe ${reads[0]} ${reads[1]}")
29 def db = (meta.kma_t_db ?: "${index}")
30 def db_basename = (db ? "${index.baseName}" : '')
31 def get_hit_accs = (meta.get_kma_hit_accs ? 'true' : 'false')
32 def res_dir = prefix + '_kma_res'
33 reads_in = (params.kmaalign_int ? "-int $reads" : "-i $reads")
34 """
35 mkdir -p $res_dir || exit 1
36 kma \\
37 $args \\
38 -t_db $db${params.fs}$db_basename \\
39 -t $task.cpus \\
40 -o $res_dir${params.fs}$prefix \\
41 $reads_in
42
43 if [ "$get_hit_accs" == "true" ]; then
44 grep -v '^#' $res_dir${params.fs}${prefix}.res | \\
45 grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > $res_dir${params.fs}${prefix}_template_hits.txt
46 fi
47
48 cat <<-END_VERSIONS > versions.yml
49 "${task.process}":
50 kma: \$( kma -v | sed -e 's%KMA-%%' )
51 END_VERSIONS
52
53 mkdirver=""
54 cutver=""
55 grepver=""
56
57 if [ "${workflow.containerEngine}" != "null" ]; then
58 mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
59 cutver="\$mkdirver"
60 grepver="\$mkdirver"
61 else
62 mkdirver=\$( mkdir --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
63 cutver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
64 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
65 fi
66
67 cat <<-END_VERSIONS >> versions.yml
68 mkdir: \$mkdirver
69 cut: \$cutver
70 grep: \$grepver
71 END_VERSIONS
72 """
73 }