nf-core_modules/modules/epang/main.nf

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process EPANG {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1':
'quay.io/biocontainers/epa-ng:0.3.8--h9a82719_1' }"
input:
tuple val(meta), path(queryaln)
path referencealn
path referencetree
path bfastfile
path splitfile
path binaryfile
output:
tuple val(meta), path("./.") , emit: epang , optional: true
tuple val(meta), path("*.epa_result.jplace.gz"), emit: jplace , optional: true
path "*.epa_info.log" , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def queryarg = queryaln ? "--query $queryaln" : ""
def refalnarg = referencealn ? "--ref-msa $referencealn" : ""
def reftreearg = referencetree ? "--tree $referencetree" : ""
def bfastarg = bfastfile ? "--bfast $bfastfile" : ""
def splitarg = splitfile ? "--split $splitfile" : ""
def binaryarg = binaryfile ? "--binary $binaryfile" : ""
if ( binaryfile && ( referencealn || referencetree ) ) error "[EPANG] Cannot supply both binary and reference MSA or reference tree. Check input"
"""
epa-ng \\
$args \\
--threads $task.cpus \\
$queryarg \\
$refalnarg \\
$reftreearg \\
$bfastarg \\
$splitarg \\
$binaryarg
if [ -e epa_result.jplace ]; then
gzip epa_result.jplace
cp epa_result.jplace.gz ${prefix}.epa_result.jplace.gz
fi
[ -e epa_info.log ] && cp epa_info.log ${prefix}.epa_info.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
epang: \$(echo \$(epa-ng --version 2>&1) | sed 's/^EPA-ng v//')
END_VERSIONS
"""
}