Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.2/modules/seqtk/seq/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
equal deleted inserted replaced
129:1bb0dacefa6d 130:04f6ac8ca13c
1 process SEQTK_SEQ {
2 tag "$meta.id"
3 label 'process_mem_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqtk${params.fs}1.3-r106" : null)
6 conda (params.enable_conda ? "bioconda::seqtk=1.3 conda-forge::gzip" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
9 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
10
11 input:
12 tuple val(meta), path(fastx)
13
14 output:
15 tuple val(meta), path("*.gz"), emit: fastx
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24
25 def extension = "fastq"
26 if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) {
27 extension = "fasta"
28 }
29 """
30 seqtk \\
31 seq \\
32 $args \\
33 $fastx | \\
34 gzip -c > ${prefix}.seqtk-seq.${task.index}.${extension}.gz
35
36 cat <<-END_VERSIONS > versions.yml
37 "${task.process}":
38 seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
39 gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' )
40 END_VERSIONS
41 """
42 }