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comparison 0.4.2/modules/seqkit/rmdup/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_RMDUP {
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
10
11 input:
12 tuple val(meta), path(reads)
13
14 output:
15 tuple val(meta), path("*duplicated.details.txt"), optional: true
16 tuple val(meta), path("*.gz") , emit: fastx
17 path "versions.yml" , emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 def rmdup_d = params.seqkit_rmdup_d ? "-d ${prefix}.seqs.duplicated.fastq.gz" : ""
26 def rmdup_D = params.seqkit_rmdup_D ? "-D ${prefix}.duplicated.details.txt" : ""
27
28 def extension = "fastq"
29 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
30 extension = "fasta"
31 }
32
33 if (meta.single_end) {
34 """
35 seqkit \\
36 rmdup \\
37 $rmdup_d \\
38 $rmdup_D \\
39 -j $task.cpus \\
40 -o ${prefix}.seqkit-rmdup.${extension}.gz \\
41 $args \\
42 $reads
43
44 cat <<-END_VERSIONS > versions.yml
45 "${task.process}":
46 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
47 END_VERSIONS
48 """
49 } else {
50 """
51 seqkit \\
52 rmdup \\
53 $rmdup_d \\
54 $rmdup_D \\
55 -j $task.cpus \\
56 -o ${prefix}.R1.seqkit-rmdup.${extension}.gz \\
57 $args \\
58 ${reads[0]}
59
60 seqkit \\
61 rmdup \\
62 $rmdup_d \\
63 $rmdup_D \\
64 -j $task.cpus \\
65 -o ${prefix}.R2.seqkit-rmdup.${extension}.gz \\
66 $args \\
67 ${reads[1]}
68
69 seqkit \\
70 pair \\
71 -j $task.cpus \\
72 -1 ${prefix}.R1.seqkit-rmdup.${extension}.gz \\
73 -2 ${prefix}.R2.seqkit-rmdup.${extension}.gz
74
75 rm ${prefix}.R1.seqkit-rmdup.${extension}.gz
76 rm ${prefix}.R2.seqkit-rmdup.${extension}.gz
77
78 cat <<-END_VERSIONS > versions.yml
79 "${task.process}":
80 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
81 END_VERSIONS
82 """
83 }
84 }