Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.6.1/modules/abricate/summary/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 ABRICATE_SUMMARY {
2 tag "${abdbs.join(',')}"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null)
6 conda (params.enable_conda ? "conda-forge::perl bioconda::abricate=1.0.1 conda-forge::coreutils" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
9 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
10
11 input:
12 tuple val(abdbs), path(abfiles)
13
14 output:
15 tuple val('abricate_ncbi'), path("*.ncbi.absum.txt") , emit: ncbi, optional: true
16 tuple val('abricate_ncbiamrplus'), path("*.ncbiamrplus.absum.txt"), emit: ncbiamrplus, optional: true
17 tuple val('abricate_resfinder'), path("*resfinder.absum.txt") , emit: resfinder, optional: true
18 tuple val('abricate_megares'), path("*.megares.absum.txt") , emit: megares, optional: true
19 tuple val('abricate_argannot'), path("*.argannot.absum.txt") , emit: argannot, optional: true
20 tuple val('abricate_ecoli_vf'), path("*.ecoli_vf.absum.txt") , emit: ecoli_vf, optional: true
21 path "versions.yml" , emit: versions
22
23 when:
24 task.ext.when == null || task.ext.when
25
26 script:
27 def args = task.ext.args ?: ''
28 def onthese = abdbs.collect{ db ->
29 abfiles.findAll { files ->
30 files =~ /\.${db}/
31 }.join(' ')
32 }.join('\\n')
33 """
34 filenum="1"
35
36 echo -e "$onthese" | while read -r files; do
37 db=\$( echo -e "\${files}" | grep -E -o '\\w+\\.ab\\.txt' | sort -u | sed -e 's/.ab.txt//' )
38
39 if [ -z "\$db" ]; then
40 db="\$filenum"
41 fi
42
43 abricate \\
44 $args \\
45 --summary \${files} \\
46 1> "abricate.\${db}.absum.txt"
47
48 sed -i -e "s/.\${db}.ab.txt//" "abricate.\${db}.absum.txt"
49 sed -i -e 's/.assembly_filtered_contigs.fasta//' "abricate.\${db}.absum.txt"
50
51 filenum=\$((filenum+1))
52 done
53
54 cat <<-END_VERSIONS > versions.yml
55 "${task.process}":
56 abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
57 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
58 END_VERSIONS
59
60 sedver=""
61 sortver=""
62 grepver=""
63
64 if [ "${workflow.containerEngine}" != "null" ]; then
65 sortver=\$( sort --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
66 sedver="\$sortver"
67 grepver="\$sortver"
68 else
69 sortver=\$( sort --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
70 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
71 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
72 fi
73
74 cat <<-END_VERSIONS >> versions.yml
75 sort: \$sortver
76 grep: \$grepver
77 sed: \$sedver
78 END_VERSIONS
79 """
80 }