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 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 """ }