nf-core_modules/modules/fastani/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FASTANI {
tag "$meta.id"
label 'process_medium'
publishDir "${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::fastani=1.32" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0"
} else {
container "quay.io/biocontainers/fastani:1.32--he1c1bb9_0"
}
input:
tuple val(meta), path(query)
path reference
output:
tuple val(meta), path("*.ani.txt"), emit: ani
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.batch_input) {
"""
fastANI \\
-ql $query \\
-rl $reference \\
-o ${prefix}.ani.txt
echo \$(fastANI --version 2>&1) | sed 's/version//;' > ${software}.version.txt
"""
} else {
"""
fastANI \\
-q $query \\
-r $reference \\
-o ${prefix}.ani.txt
echo \$(fastANI --version 2>&1) | sed 's/version//;' > ${software}.version.txt
"""
}
}