Mercurial > repos > kkonganti > cfsan_cronology
comparison 0.1.0/modules/prodigal/main.nf @ 0:c8597e9e1a97
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 12:37:44 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:c8597e9e1a97 |
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| 1 process PRODIGAL { | |
| 2 tag "$meta.id" | |
| 3 label 'process_nano' | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}prodigal${params.fs}2.6.3" : null) | |
| 6 conda (params.enable_conda ? "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : | |
| 9 'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }" | |
| 10 | |
| 11 input: | |
| 12 tuple val(meta), path(genome) | |
| 13 val(output_format) | |
| 14 | |
| 15 output: | |
| 16 tuple val(meta), path("*.${output_format}"), emit: gene_annotations | |
| 17 tuple val(meta), path("*.fna") , emit: cds | |
| 18 tuple val(meta), path("*.faa") , emit: proteins | |
| 19 tuple val(meta), path("*_all.txt") , emit: all_gene_annotations | |
| 20 tuple val(meta), path("*trn") , emit: trained, optional: true | |
| 21 path "versions.yml" , emit: versions | |
| 22 | |
| 23 when: | |
| 24 task.ext.when == null || task.ext.when | |
| 25 | |
| 26 script: | |
| 27 def args = task.ext.args ?: '' | |
| 28 def prefix = task.ext.prefix ?: "${meta.id}" | |
| 29 def training = args.toString().matches(/.*-t/) ? "-t ${prefix}.trn" : '' | |
| 30 args = args.toString().replace(/-t/, '') | |
| 31 """ | |
| 32 if [ "$training" = "-t ${prefix}.trn" ]; then | |
| 33 touch "${prefix}.fna" | |
| 34 touch "${prefix}.faa" | |
| 35 touch "${prefix}_all.txt" | |
| 36 touch "${prefix}.${output_format}" | |
| 37 | |
| 38 prodigal \\ | |
| 39 $training \\ | |
| 40 -i $genome | |
| 41 fi | |
| 42 | |
| 43 prodigal \\ | |
| 44 $args \\ | |
| 45 -d "${prefix}.fna" \\ | |
| 46 -o "${prefix}.${output_format}" \\ | |
| 47 -a "${prefix}.faa" \\ | |
| 48 -s "${prefix}_all.txt" \\ | |
| 49 -i $genome | |
| 50 | |
| 51 cat <<-END_VERSIONS > versions.yml | |
| 52 "${task.process}": | |
| 53 prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p') | |
| 54 END_VERSIONS | |
| 55 """ | |
| 56 } |