nf-core_modules/modules/nextclade/main.nf
Mahesh Binzer-Panchal d473a247d2
Replace remaining task.ext.suffix with task.ext.prefix (#1117)
* Replace remaining task.ext.suffix with task.ext.prefix
2021-12-07 15:00:43 +01:00

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process NEXTCLADE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::nextclade_js=0.14.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0' :
'quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0' }"
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("${prefix}.csv") , emit: csv
tuple val(meta), path("${prefix}.json") , emit: json
tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
tuple val(meta), path("${prefix}.tsv") , emit: tsv
tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
nextclade \\
$args \\
--jobs $task.cpus \\
--input-fasta $fasta \\
--output-json ${prefix}.json \\
--output-csv ${prefix}.csv \\
--output-tsv ${prefix}.tsv \\
--output-tsv-clades-only ${prefix}.clades.tsv \\
--output-tree ${prefix}.tree.json
cat <<-END_VERSIONS > versions.yml
"${task.process}":
nextclade: \$(nextclade --version 2>&1)
END_VERSIONS
"""
}