cfsan_centriflaken: 0.4.2/modules/mlst/main.nf annotate

planemo upload

rev	line source
kkonganti@105	1 process MLST {
kkonganti@105	2 tag "$meta.id"
kkonganti@105	3 label 'process_low'
kkonganti@105	4
kkonganti@105	5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.19.0" : null)
kkonganti@105	6 conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null)
kkonganti@105	7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105	8 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' :
kkonganti@105	9 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }"
kkonganti@105	10
kkonganti@105	11 input:
kkonganti@105	12 tuple val(meta), path(fasta)
kkonganti@105	13
kkonganti@105	14 output:
kkonganti@105	15 tuple val(meta), path("*.tsv"), emit: tsv
kkonganti@105	16 path "versions.yml" , emit: versions
kkonganti@105	17
kkonganti@105	18 when:
kkonganti@105	19 (task.ext.when == null \|\| task.ext.when) && fasta.size() > 0
kkonganti@105	20
kkonganti@105	21 script:
kkonganti@105	22 def args = task.ext.args ?: ''
kkonganti@105	23 def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105	24 """
kkonganti@105	25 mlst \\
kkonganti@105	26 --threads $task.cpus \\
kkonganti@105	27 $args \\
kkonganti@105	28 $fasta > ${prefix}.tsv
kkonganti@105	29
kkonganti@105	30 cat <<-END_VERSIONS > versions.yml
kkonganti@105	31 "${task.process}":
kkonganti@105	32 mlst: \$( echo \$(mlst --version 2>&1) \| sed 's/mlst //' )
kkonganti@105	33 END_VERSIONS
kkonganti@105	34 """
kkonganti@105	35
kkonganti@105	36 }

Mercurial > repos > kkonganti > cfsan_centriflaken