Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.2/modules/centrifuge/extract/main.nf @ 130:04f6ac8ca13c

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
parents 52045ea4679d
children
comparison
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129:1bb0dacefa6d 130:04f6ac8ca13c
1 process CENTRIFUGE_EXTRACT {
2 tag "$meta.id"
3 label 'process_low'
4
5 //seqkit container contains required bash and other utilities
6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
7 conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::coreutils" : null)
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
9 'https://depot.galaxyproject.org/singularity/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0':
10 'quay.io/biocontainers/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0' }"
11
12 input:
13 tuple val(meta), path(centrifuge_report)
14 tuple val(meta), path(centrifuge_output)
15
16 output:
17 tuple val(meta), path('*.extract-centrifuge-bug-ids.txt'), emit: extracted
18 path "versions.yml" , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}"
26 """
27 grep -F '${params.centrifuge_extract_bug}' $centrifuge_report \
28 | cut -f2 \
29 | sort -u \
30 | while read -r taxId; do
31 echo -e "\t\$taxId"'\$'
32 done > gotcha.txt
33
34 cut -f1-3 $centrifuge_output | grep -E -f gotcha.txt | cut -f1 | sort -u > ${prefix}.extract-centrifuge-bug-ids.txt || true
35
36 cat <<-END_VERSIONS > versions.yml
37 "${task.process}":
38 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
39 END_VERSIONS
40
41 ver=""
42 sedver=""
43
44 if [ "${workflow.containerEngine}" != "null" ]; then
45 ver=\$( cut --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
46 sedver="\$ver"
47 else
48 ver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
49 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
50 fi
51
52 cat <<-END_VERSIONS >> versions.yml
53 cut: \$ver
54 tail: \$ver
55 sort: \$ver
56 sed: \$sedver
57 END_VERSIONS
58 """
59 }