Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/modules/amrfinderplus/run/main.nf @ 105:52045ea4679d
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 27 Jun 2024 14:17:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 process AMRFINDERPLUS_RUN { |
| kkonganti@105 | 2 tag "$meta.id" |
| kkonganti@105 | 3 label 'process_low' |
| kkonganti@105 | 4 |
| kkonganti@105 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}amrfinderplus${params.fs}3.10.24" : null) |
| kkonganti@105 | 6 conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.24 conda-forge::libgcc-ng" : null) |
| kkonganti@105 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@105 | 8 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0': |
| kkonganti@105 | 9 'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }" |
| kkonganti@105 | 10 |
| kkonganti@105 | 11 input: |
| kkonganti@105 | 12 tuple val(meta), path(fasta) |
| kkonganti@105 | 13 |
| kkonganti@105 | 14 output: |
| kkonganti@105 | 15 tuple val(meta), path("${prefix}.tsv") , emit: report |
| kkonganti@105 | 16 tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true |
| kkonganti@105 | 17 path "versions.yml" , emit: versions |
| kkonganti@105 | 18 |
| kkonganti@105 | 19 when: |
| kkonganti@105 | 20 (task.ext.when == null || task.ext.when) && fasta.size() > 0 |
| kkonganti@105 | 21 |
| kkonganti@105 | 22 script: |
| kkonganti@105 | 23 def args = task.ext.args ?: '' |
| kkonganti@105 | 24 def is_compressed = fasta.getName().endsWith(".gz") ? true : false |
| kkonganti@105 | 25 prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@105 | 26 organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : "" |
| kkonganti@105 | 27 fasta_name = fasta.getName().replace(".gz", "") |
| kkonganti@105 | 28 fasta_param = "-n" |
| kkonganti@105 | 29 if (meta.containsKey("is_proteins")) { |
| kkonganti@105 | 30 if (meta.is_proteins) { |
| kkonganti@105 | 31 fasta_param = "-p" |
| kkonganti@105 | 32 } |
| kkonganti@105 | 33 } |
| kkonganti@105 | 34 """ |
| kkonganti@105 | 35 if [ "$is_compressed" == "true" ]; then |
| kkonganti@105 | 36 gzip -c -d $fasta > $fasta_name |
| kkonganti@105 | 37 fi |
| kkonganti@105 | 38 |
| kkonganti@105 | 39 amrfinder \\ |
| kkonganti@105 | 40 $fasta_param $fasta_name \\ |
| kkonganti@105 | 41 $organism_param \\ |
| kkonganti@105 | 42 $args \\ |
| kkonganti@105 | 43 --threads $task.cpus > ${prefix}.tsv |
| kkonganti@105 | 44 |
| kkonganti@105 | 45 |
| kkonganti@105 | 46 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 47 "${task.process}": |
| kkonganti@105 | 48 amrfinderplus: \$(amrfinder --version) |
| kkonganti@105 | 49 gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' ) |
| kkonganti@105 | 50 END_VERSIONS |
| kkonganti@105 | 51 """ |
| kkonganti@105 | 52 } |