Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/seqkit/seq/main.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process SEQKIT_SEQ {
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" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
10
11 input:
12 tuple val(meta), path(reads)
13
14 output:
15 tuple val(meta), path("*.gz"), emit: fastx
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${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 seqkit \\
33 seq \\
34 -j $task.cpus \\
35 -o ${prefix}.seqkit-seq.${extension}.gz \\
36 $args \\
37 $reads
38
39 cat <<-END_VERSIONS > versions.yml
40 "${task.process}":
41 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
42 END_VERSIONS
43 """
44 } else {
45 """
46 seqkit \\
47 seq \\
48 -j $task.cpus \\
49 -o ${prefix}.R1.seqkit-seq.${extension}.gz \\
50 $args \\
51 ${reads[0]}
52
53 seqkit \\
54 seq \\
55 -j $task.cpus \\
56 -o ${prefix}.R2.seqkit-seq.${extension}.gz \\
57 $args \\
58 ${reads[1]}
59
60 seqkit \\
61 pair \\
62 -j $task.cpus \\
63 -1 ${prefix}.R1.seqkit-seq.${extension}.gz \\
64 -2 ${prefix}.R2.seqkit-seq.${extension}.gz
65
66 rm ${prefix}.R1.seqkit-seq.${extension}.gz
67 rm ${prefix}.R2.seqkit-seq.${extension}.gz
68
69 cat <<-END_VERSIONS > versions.yml
70 "${task.process}":
71 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
72 END_VERSIONS
73 """
74 }
75 }