Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/modules/seqkit/grep/main.nf @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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kkonganti@105 1 process SEQKIT_GREP {
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 conda-forge::sed=4.7 conda-forge::coreutils" : null)
kkonganti@105 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105 8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
kkonganti@105 9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
kkonganti@105 10
kkonganti@105 11 input:
kkonganti@105 12 tuple val(meta), path(reads), path(pattern_file)
kkonganti@105 13
kkonganti@105 14 output:
kkonganti@105 15 tuple val(meta), path("*.gz"), emit: fastx
kkonganti@105 16 path "versions.yml" , emit: versions
kkonganti@105 17
kkonganti@105 18 when:
kkonganti@105 19 task.ext.when == null || task.ext.when
kkonganti@105 20
kkonganti@105 21 script:
kkonganti@105 22 def args = task.ext.args ?: ''
kkonganti@105 23 def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105 24
kkonganti@105 25 def extension = "fastq"
kkonganti@105 26 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
kkonganti@105 27 extension = "fasta"
kkonganti@105 28 }
kkonganti@105 29
kkonganti@105 30 if (meta.single_end) {
kkonganti@105 31 """
kkonganti@105 32 pattern_file_contents=\$(sed '1!d' $pattern_file)
kkonganti@105 33 if [ "\$pattern_file_contents" != "DuMmY" ]; then
kkonganti@105 34 additional_args="-f $pattern_file $args"
kkonganti@105 35 else
kkonganti@105 36 additional_args="$args"
kkonganti@105 37 fi
kkonganti@105 38
kkonganti@105 39 seqkit \\
kkonganti@105 40 grep \\
kkonganti@105 41 -j $task.cpus \\
kkonganti@105 42 -o ${prefix}.seqkit-grep.${extension}.gz \\
kkonganti@105 43 \$additional_args \\
kkonganti@105 44 $reads
kkonganti@105 45
kkonganti@105 46 cat <<-END_VERSIONS > versions.yml
kkonganti@105 47 "${task.process}":
kkonganti@105 48 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
kkonganti@105 49 END_VERSIONS
kkonganti@105 50 """
kkonganti@105 51 } else {
kkonganti@105 52 """
kkonganti@105 53 pattern_file_contents=\$(sed '1!d' $pattern_file)
kkonganti@105 54 if [ "\$pattern_file_contents" != "DuMmY" ]; then
kkonganti@105 55 additional_args="-f $pattern_file $args"
kkonganti@105 56 else
kkonganti@105 57 additional_args="$args"
kkonganti@105 58 fi
kkonganti@105 59
kkonganti@105 60 seqkit \\
kkonganti@105 61 grep \\
kkonganti@105 62 -j $task.cpus \\
kkonganti@105 63 -o ${prefix}.R1.seqkit-grep.${extension}.gz \\
kkonganti@105 64 \$additional_args \\
kkonganti@105 65 ${reads[0]}
kkonganti@105 66
kkonganti@105 67 seqkit \\
kkonganti@105 68 grep \\
kkonganti@105 69 -j $task.cpus \\
kkonganti@105 70 -o ${prefix}.R2.seqkit-grep.${extension}.gz \\
kkonganti@105 71 \$additional_args \\
kkonganti@105 72 ${reads[1]}
kkonganti@105 73
kkonganti@105 74 seqkit \\
kkonganti@105 75 pair \\
kkonganti@105 76 -j $task.cpus \\
kkonganti@105 77 -1 ${prefix}.R1.seqkit-grep.${extension}.gz \\
kkonganti@105 78 -2 ${prefix}.R2.seqkit-grep.${extension}.gz
kkonganti@105 79
kkonganti@105 80 rm ${prefix}.R1.seqkit-grep.${extension}.gz
kkonganti@105 81 rm ${prefix}.R2.seqkit-grep.${extension}.gz
kkonganti@105 82
kkonganti@105 83 cat <<-END_VERSIONS > versions.yml
kkonganti@105 84 "${task.process}":
kkonganti@105 85 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
kkonganti@105 86 END_VERSIONS
kkonganti@105 87 """
kkonganti@105 88 }
kkonganti@105 89 }