nf-core_modules/modules/agrvate/main.nf
Robert A. Petit III 8e9d6cd5e4
Update agrvate to latest version (#728)
The new version of agrvate fixes an issue where sample names with a `.` (dot) in there names caused the name to be truncated

https://github.com/VishnuRaghuram94/AgrVATE/releases/tag/v1.0.1

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 20:28:53 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process AGRVATE {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::agrvate=1.0.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/agrvate:1.0.1--hdfd78af_0"
} else {
container "quay.io/biocontainers/agrvate:1.0.1--hdfd78af_0"
}
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary
path "${fasta.baseName}-results" , emit: results_dir
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
agrvate \\
$options.args \\
-i $fasta
echo \$(agrvate -v 2>&1) | sed 's/agrvate //;' > ${software}.version.txt
"""
}