Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/modules/cat/fastq/main.nf @ 130:04f6ac8ca13c

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
parents 52045ea4679d
children
rev   line source
kkonganti@105 1 process CAT_FASTQ {
kkonganti@105 2 tag "$meta.id"
kkonganti@105 3 label 'process_micro'
kkonganti@105 4
kkonganti@105 5 conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::gzip" : null)
kkonganti@105 6 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105 7 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
kkonganti@105 8 'biocontainers/biocontainers:v1.2.0_cv1' }"
kkonganti@105 9
kkonganti@105 10 input:
kkonganti@105 11 tuple val(meta), path(reads, stageAs: "input*/*")
kkonganti@105 12
kkonganti@105 13 output:
kkonganti@105 14 tuple val(meta), path("*.merged.fastq.gz"), emit: catted_reads
kkonganti@105 15 path "versions.yml" , emit: versions
kkonganti@105 16
kkonganti@105 17 when:
kkonganti@105 18 task.ext.when == null || task.ext.when
kkonganti@105 19
kkonganti@105 20 script:
kkonganti@105 21 def args = task.ext.args ?: ''
kkonganti@105 22 def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105 23 def readList = reads.collect{ it.toString() }
kkonganti@105 24 def is_in_gz = readList[0].endsWith('.gz')
kkonganti@105 25 def gz_or_ungz = (is_in_gz ? '' : ' | gzip')
kkonganti@105 26 def pigz_or_ungz = (is_in_gz ? '' : " | pigz -p ${task.cpus}")
kkonganti@105 27 if (meta.single_end) {
kkonganti@105 28 if (readList.size > 1) {
kkonganti@105 29 """
kkonganti@105 30 zcmd="gzip"
kkonganti@105 31 zver=""
kkonganti@105 32
kkonganti@105 33 if type pigz > /dev/null 2>&1; then
kkonganti@105 34 cat ${readList.join(' ')} ${pigz_or_ungz} > ${prefix}.merged.fastq.gz
kkonganti@105 35 zcmd="pigz"
kkonganti@105 36 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@105 37 else
kkonganti@105 38 cat ${readList.join(' ')} ${gz_or_ungz} > ${prefix}.merged.fastq.gz
kkonganti@105 39 zcmd="gzip"
kkonganti@105 40
kkonganti@105 41 if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@105 42 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@105 43 else
kkonganti@105 44 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@105 45 fi
kkonganti@105 46 fi
kkonganti@105 47
kkonganti@105 48 cat <<-END_VERSIONS > versions.yml
kkonganti@105 49 "${task.process}":
kkonganti@105 50 cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
kkonganti@105 51 \$zcmd: \$zver
kkonganti@105 52 END_VERSIONS
kkonganti@105 53 """
kkonganti@105 54 }
kkonganti@105 55 } else {
kkonganti@105 56 if (readList.size > 2) {
kkonganti@105 57 def read1 = []
kkonganti@105 58 def read2 = []
kkonganti@105 59 readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
kkonganti@105 60 """
kkonganti@105 61 zcmd="gzip"
kkonganti@105 62 zver=""
kkonganti@105 63
kkonganti@105 64 if type pigz > /dev/null 2>&1; then
kkonganti@105 65 cat ${read1.join(' ')} ${pigz_or_ungz} > ${prefix}_1.merged.fastq.gz
kkonganti@105 66 cat ${read2.join(' ')} ${pigz_or_ungz} > ${prefix}_2.merged.fastq.gz
kkonganti@105 67 zcmd="pigz"
kkonganti@105 68 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@105 69 else
kkonganti@105 70 cat ${read1.join(' ')} ${gz_or_ungz} > ${prefix}_1.merged.fastq.gz
kkonganti@105 71 cat ${read2.join(' ')} ${gz_or_ungz} > ${prefix}_2.merged.fastq.gz
kkonganti@105 72 zcmd="gzip"
kkonganti@105 73
kkonganti@105 74 if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@105 75 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@105 76 else
kkonganti@105 77 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@105 78 fi
kkonganti@105 79 fi
kkonganti@105 80
kkonganti@105 81 cat <<-END_VERSIONS > versions.yml
kkonganti@105 82 "${task.process}":
kkonganti@105 83 cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
kkonganti@105 84 \$zcmd: \$zver
kkonganti@105 85 END_VERSIONS
kkonganti@105 86 """
kkonganti@105 87 }
kkonganti@105 88 }
kkonganti@105 89 }