Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/abricate/run/main.nf @ 19:4b304d77bbfb
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 11:20:22 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 process ABRICATE_RUN { |
| kkonganti@17 | 2 tag "$meta.id" |
| kkonganti@17 | 3 label 'process_micro' |
| kkonganti@17 | 4 |
| kkonganti@17 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null) |
| kkonganti@17 | 6 conda (params.enable_conda ? "conda-forge::perl bioconda::abricate=1.0.1" : null) |
| kkonganti@17 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@17 | 8 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': |
| kkonganti@17 | 9 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }" |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 input: |
| kkonganti@17 | 12 tuple val(meta), path(assembly) |
| kkonganti@17 | 13 val abdbs |
| kkonganti@17 | 14 |
| kkonganti@17 | 15 output: |
| kkonganti@17 | 16 path "${meta.id}${params.fs}*" |
| kkonganti@17 | 17 tuple val(meta), path("${meta.id}${params.fs}*.ab.txt"), emit: abricated |
| kkonganti@17 | 18 path "versions.yml" , emit: versions |
| kkonganti@17 | 19 |
| kkonganti@17 | 20 when: |
| kkonganti@17 | 21 (task.ext.when == null || task.ext.when) && assembly.size() > 0 |
| kkonganti@17 | 22 |
| kkonganti@17 | 23 script: |
| kkonganti@17 | 24 def args = task.ext.args ?: '' |
| kkonganti@17 | 25 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@17 | 26 def dbs = abdbs.collect().join('\\n') |
| kkonganti@17 | 27 """ |
| kkonganti@17 | 28 newprefix="${prefix}${params.fs}${prefix}" |
| kkonganti@17 | 29 |
| kkonganti@17 | 30 if [ ! -d "$prefix" ]; then |
| kkonganti@17 | 31 mkdir "$prefix" || exit 1 |
| kkonganti@17 | 32 fi |
| kkonganti@17 | 33 |
| kkonganti@17 | 34 echo -e "$dbs" | while read -r db; do |
| kkonganti@17 | 35 abricate \\ |
| kkonganti@17 | 36 $assembly \\ |
| kkonganti@17 | 37 $args \\ |
| kkonganti@17 | 38 --db \$db \\ |
| kkonganti@17 | 39 --threads $task.cpus 1> "\${newprefix}.\${db}.ab.txt" |
| kkonganti@17 | 40 done |
| kkonganti@17 | 41 |
| kkonganti@17 | 42 cat <<-END_VERSIONS > versions.yml |
| kkonganti@17 | 43 "${task.process}": |
| kkonganti@17 | 44 abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' ) |
| kkonganti@17 | 45 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) |
| kkonganti@17 | 46 END_VERSIONS |
| kkonganti@17 | 47 """ |
| kkonganti@17 | 48 } |