Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/modules/seqkit/grep/main.nf @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 process SEQKIT_GREP {
2 tag "$meta.id"
3 label 'process_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null)
6 conda (params.enable_conda ? "bioconda::seqkit=2.2.0 conda-forge::sed=4.7 conda-forge::coreutils" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
10
11 input:
12 tuple val(meta), path(reads), path(pattern_file)
13
14 output:
15 tuple val(meta), path("*.gz"), emit: fastx
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24
25 def extension = "fastq"
26 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
27 extension = "fasta"
28 }
29
30 if (meta.single_end) {
31 """
32 pattern_file_contents=\$(sed '1!d' $pattern_file)
33 if [ "\$pattern_file_contents" != "DuMmY" ]; then
34 additional_args="-f $pattern_file $args"
35 else
36 additional_args="$args"
37 fi
38
39 seqkit \\
40 grep \\
41 -j $task.cpus \\
42 -o ${prefix}.seqkit-grep.${extension}.gz \\
43 \$additional_args \\
44 $reads
45
46 cat <<-END_VERSIONS > versions.yml
47 "${task.process}":
48 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
49 END_VERSIONS
50 """
51 } else {
52 """
53 pattern_file_contents=\$(sed '1!d' $pattern_file)
54 if [ "\$pattern_file_contents" != "DuMmY" ]; then
55 additional_args="-f $pattern_file $args"
56 else
57 additional_args="$args"
58 fi
59
60 seqkit \\
61 grep \\
62 -j $task.cpus \\
63 -o ${prefix}.R1.seqkit-grep.${extension}.gz \\
64 \$additional_args \\
65 ${reads[0]}
66
67 seqkit \\
68 grep \\
69 -j $task.cpus \\
70 -o ${prefix}.R2.seqkit-grep.${extension}.gz \\
71 \$additional_args \\
72 ${reads[1]}
73
74 seqkit \\
75 pair \\
76 -j $task.cpus \\
77 -1 ${prefix}.R1.seqkit-grep.${extension}.gz \\
78 -2 ${prefix}.R2.seqkit-grep.${extension}.gz
79
80 rm ${prefix}.R1.seqkit-grep.${extension}.gz
81 rm ${prefix}.R2.seqkit-grep.${extension}.gz
82
83 cat <<-END_VERSIONS > versions.yml
84 "${task.process}":
85 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
86 END_VERSIONS
87 """
88 }
89 }