Mercurial > repos > kkonganti > cfsan_bettercallsal
comparison 0.5.0/modules/cat/fastq/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
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| 0:a4b1ee4b68b1 | 1:365849f031fd |
|---|---|
| 1 process CAT_FASTQ { | |
| 2 tag "$meta.id" | |
| 3 label 'process_micro' | |
| 4 | |
| 5 conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::gzip" : null) | |
| 6 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 7 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : | |
| 8 'biocontainers/biocontainers:v1.2.0_cv1' }" | |
| 9 | |
| 10 input: | |
| 11 tuple val(meta), path(reads, stageAs: "input*/*") | |
| 12 | |
| 13 output: | |
| 14 tuple val(meta), path("*.merged.fastq.gz"), emit: catted_reads | |
| 15 path "versions.yml" , emit: versions | |
| 16 | |
| 17 when: | |
| 18 task.ext.when == null || task.ext.when | |
| 19 | |
| 20 script: | |
| 21 def args = task.ext.args ?: '' | |
| 22 def prefix = task.ext.prefix ?: "${meta.id}" | |
| 23 def readList = reads.collect{ it.toString() } | |
| 24 def is_in_gz = readList[0].endsWith('.gz') | |
| 25 def gz_or_ungz = (is_in_gz ? '' : ' | gzip') | |
| 26 def pigz_or_ungz = (is_in_gz ? '' : " | pigz -p ${task.cpus}") | |
| 27 if (meta.single_end) { | |
| 28 if (readList.size > 1) { | |
| 29 """ | |
| 30 zcmd="gzip" | |
| 31 zver="" | |
| 32 | |
| 33 if type pigz > /dev/null 2>&1; then | |
| 34 cat ${readList.join(' ')} ${pigz_or_ungz} > ${prefix}.merged.fastq.gz | |
| 35 zcmd="pigz" | |
| 36 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) | |
| 37 else | |
| 38 cat ${readList.join(' ')} ${gz_or_ungz} > ${prefix}.merged.fastq.gz | |
| 39 zcmd="gzip" | |
| 40 | |
| 41 if [ "${workflow.containerEngine}" != "null" ]; then | |
| 42 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) | |
| 43 else | |
| 44 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) | |
| 45 fi | |
| 46 fi | |
| 47 | |
| 48 cat <<-END_VERSIONS > versions.yml | |
| 49 "${task.process}": | |
| 50 cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' ) | |
| 51 \$zcmd: \$zver | |
| 52 END_VERSIONS | |
| 53 """ | |
| 54 } | |
| 55 } else { | |
| 56 if (readList.size > 2) { | |
| 57 def read1 = [] | |
| 58 def read2 = [] | |
| 59 readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v } | |
| 60 """ | |
| 61 zcmd="gzip" | |
| 62 zver="" | |
| 63 | |
| 64 if type pigz > /dev/null 2>&1; then | |
| 65 cat ${read1.join(' ')} ${pigz_or_ungz} > ${prefix}_1.merged.fastq.gz | |
| 66 cat ${read2.join(' ')} ${pigz_or_ungz} > ${prefix}_2.merged.fastq.gz | |
| 67 zcmd="pigz" | |
| 68 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) | |
| 69 else | |
| 70 cat ${read1.join(' ')} ${gz_or_ungz} > ${prefix}_1.merged.fastq.gz | |
| 71 cat ${read2.join(' ')} ${gz_or_ungz} > ${prefix}_2.merged.fastq.gz | |
| 72 zcmd="gzip" | |
| 73 | |
| 74 if [ "${workflow.containerEngine}" != "null" ]; then | |
| 75 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) | |
| 76 else | |
| 77 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) | |
| 78 fi | |
| 79 fi | |
| 80 | |
| 81 cat <<-END_VERSIONS > versions.yml | |
| 82 "${task.process}": | |
| 83 cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' ) | |
| 84 \$zcmd: \$zver | |
| 85 END_VERSIONS | |
| 86 """ | |
| 87 } | |
| 88 } | |
| 89 } |