|
kkonganti@105
|
1 process CENTRIFUGE_EXTRACT {
|
|
kkonganti@105
|
2 tag "$meta.id"
|
|
kkonganti@105
|
3 label 'process_low'
|
|
kkonganti@105
|
4
|
|
kkonganti@105
|
5 //seqkit container contains required bash and other utilities
|
|
kkonganti@105
|
6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
|
|
kkonganti@105
|
7 conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::coreutils" : null)
|
|
kkonganti@105
|
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
kkonganti@105
|
9 'https://depot.galaxyproject.org/singularity/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0':
|
|
kkonganti@105
|
10 'quay.io/biocontainers/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0' }"
|
|
kkonganti@105
|
11
|
|
kkonganti@105
|
12 input:
|
|
kkonganti@105
|
13 tuple val(meta), path(centrifuge_report)
|
|
kkonganti@105
|
14 tuple val(meta), path(centrifuge_output)
|
|
kkonganti@105
|
15
|
|
kkonganti@105
|
16 output:
|
|
kkonganti@105
|
17 tuple val(meta), path('*.extract-centrifuge-bug-ids.txt'), emit: extracted
|
|
kkonganti@105
|
18 path "versions.yml" , emit: versions
|
|
kkonganti@105
|
19
|
|
kkonganti@105
|
20 when:
|
|
kkonganti@105
|
21 task.ext.when == null || task.ext.when
|
|
kkonganti@105
|
22
|
|
kkonganti@105
|
23 script:
|
|
kkonganti@105
|
24 def args = task.ext.args ?: ''
|
|
kkonganti@105
|
25 def prefix = task.ext.prefix ?: "${meta.id}"
|
|
kkonganti@105
|
26 """
|
|
kkonganti@105
|
27 grep -F '${params.centrifuge_extract_bug}' $centrifuge_report \
|
|
kkonganti@105
|
28 | cut -f2 \
|
|
kkonganti@105
|
29 | sort -u \
|
|
kkonganti@105
|
30 | while read -r taxId; do
|
|
kkonganti@105
|
31 echo -e "\t\$taxId"'\$'
|
|
kkonganti@105
|
32 done > gotcha.txt
|
|
kkonganti@105
|
33
|
|
kkonganti@105
|
34 cut -f1-3 $centrifuge_output | grep -E -f gotcha.txt | cut -f1 | sort -u > ${prefix}.extract-centrifuge-bug-ids.txt || true
|
|
kkonganti@105
|
35
|
|
kkonganti@105
|
36 cat <<-END_VERSIONS > versions.yml
|
|
kkonganti@105
|
37 "${task.process}":
|
|
kkonganti@105
|
38 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
|
|
kkonganti@105
|
39 END_VERSIONS
|
|
kkonganti@105
|
40
|
|
kkonganti@105
|
41 ver=""
|
|
kkonganti@105
|
42 sedver=""
|
|
kkonganti@105
|
43
|
|
kkonganti@105
|
44 if [ "${workflow.containerEngine}" != "null" ]; then
|
|
kkonganti@105
|
45 ver=\$( cut --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
|
|
kkonganti@105
|
46 sedver="\$ver"
|
|
kkonganti@105
|
47 else
|
|
kkonganti@105
|
48 ver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
|
|
kkonganti@105
|
49 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
|
|
kkonganti@105
|
50 fi
|
|
kkonganti@105
|
51
|
|
kkonganti@105
|
52 cat <<-END_VERSIONS >> versions.yml
|
|
kkonganti@105
|
53 cut: \$ver
|
|
kkonganti@105
|
54 tail: \$ver
|
|
kkonganti@105
|
55 sort: \$ver
|
|
kkonganti@105
|
56 sed: \$sedver
|
|
kkonganti@105
|
57 END_VERSIONS
|
|
kkonganti@105
|
58 """
|
|
kkonganti@105
|
59 } |
