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annotate 0.4.2/modules/seqkit/rmdup/main.nf @ 143:620bffa66bbb tip

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planemo upload
author kkonganti
date Thu, 11 Jul 2024 14:48:07 -0400
parents 52045ea4679d
children
rev   line source
kkonganti@105 1 process SEQKIT_RMDUP {
kkonganti@105 2 tag "$meta.id"
kkonganti@105 3 label 'process_low'
kkonganti@105 4
kkonganti@105 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null)
kkonganti@105 6 conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
kkonganti@105 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105 8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
kkonganti@105 9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
kkonganti@105 10
kkonganti@105 11 input:
kkonganti@105 12 tuple val(meta), path(reads)
kkonganti@105 13
kkonganti@105 14 output:
kkonganti@105 15 tuple val(meta), path("*duplicated.details.txt"), optional: true
kkonganti@105 16 tuple val(meta), path("*.gz") , emit: fastx
kkonganti@105 17 path "versions.yml" , emit: versions
kkonganti@105 18
kkonganti@105 19 when:
kkonganti@105 20 task.ext.when == null || task.ext.when
kkonganti@105 21
kkonganti@105 22 script:
kkonganti@105 23 def args = task.ext.args ?: ''
kkonganti@105 24 def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105 25 def rmdup_d = params.seqkit_rmdup_d ? "-d ${prefix}.seqs.duplicated.fastq.gz" : ""
kkonganti@105 26 def rmdup_D = params.seqkit_rmdup_D ? "-D ${prefix}.duplicated.details.txt" : ""
kkonganti@105 27
kkonganti@105 28 def extension = "fastq"
kkonganti@105 29 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
kkonganti@105 30 extension = "fasta"
kkonganti@105 31 }
kkonganti@105 32
kkonganti@105 33 if (meta.single_end) {
kkonganti@105 34 """
kkonganti@105 35 seqkit \\
kkonganti@105 36 rmdup \\
kkonganti@105 37 $rmdup_d \\
kkonganti@105 38 $rmdup_D \\
kkonganti@105 39 -j $task.cpus \\
kkonganti@105 40 -o ${prefix}.seqkit-rmdup.${extension}.gz \\
kkonganti@105 41 $args \\
kkonganti@105 42 $reads
kkonganti@105 43
kkonganti@105 44 cat <<-END_VERSIONS > versions.yml
kkonganti@105 45 "${task.process}":
kkonganti@105 46 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
kkonganti@105 47 END_VERSIONS
kkonganti@105 48 """
kkonganti@105 49 } else {
kkonganti@105 50 """
kkonganti@105 51 seqkit \\
kkonganti@105 52 rmdup \\
kkonganti@105 53 $rmdup_d \\
kkonganti@105 54 $rmdup_D \\
kkonganti@105 55 -j $task.cpus \\
kkonganti@105 56 -o ${prefix}.R1.seqkit-rmdup.${extension}.gz \\
kkonganti@105 57 $args \\
kkonganti@105 58 ${reads[0]}
kkonganti@105 59
kkonganti@105 60 seqkit \\
kkonganti@105 61 rmdup \\
kkonganti@105 62 $rmdup_d \\
kkonganti@105 63 $rmdup_D \\
kkonganti@105 64 -j $task.cpus \\
kkonganti@105 65 -o ${prefix}.R2.seqkit-rmdup.${extension}.gz \\
kkonganti@105 66 $args \\
kkonganti@105 67 ${reads[1]}
kkonganti@105 68
kkonganti@105 69 seqkit \\
kkonganti@105 70 pair \\
kkonganti@105 71 -j $task.cpus \\
kkonganti@105 72 -1 ${prefix}.R1.seqkit-rmdup.${extension}.gz \\
kkonganti@105 73 -2 ${prefix}.R2.seqkit-rmdup.${extension}.gz
kkonganti@105 74
kkonganti@105 75 rm ${prefix}.R1.seqkit-rmdup.${extension}.gz
kkonganti@105 76 rm ${prefix}.R2.seqkit-rmdup.${extension}.gz
kkonganti@105 77
kkonganti@105 78 cat <<-END_VERSIONS > versions.yml
kkonganti@105 79 "${task.process}":
kkonganti@105 80 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
kkonganti@105 81 END_VERSIONS
kkonganti@105 82 """
kkonganti@105 83 }
kkonganti@105 84 }