mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
process HICAP {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' :
|
|
'quay.io/biocontainers/hicap:1.0.3--py_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
path database_dir
|
|
path model_fp
|
|
|
|
output:
|
|
tuple val(meta), path("*.gbk"), emit: gbk, optional: true
|
|
tuple val(meta), path("*.svg"), emit: svg, optional: true
|
|
tuple val(meta), path("*.tsv"), emit: tsv, optional: true
|
|
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 database_args = database_dir ? "--database_dir ${database_dir}" : ""
|
|
def model_args = model_fp ? "--model_fp ${model_fp}" : ""
|
|
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
|
|
def fasta_name = fasta.getName().replace(".gz", "")
|
|
"""
|
|
if [ "$is_compressed" == "true" ]; then
|
|
gzip -c -d $fasta > $fasta_name
|
|
fi
|
|
hicap \\
|
|
--query_fp $fasta_name \\
|
|
$database_args \\
|
|
$model_args \\
|
|
$args \\
|
|
--threads $task.cpus \\
|
|
-o ./
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
hicap: \$( echo \$( hicap --version 2>&1 ) | sed 's/^.*hicap //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|