process SRATOOLS_PREFETCH { tag "$id" label 'process_low' label 'error_retry' conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' : 'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }" input: tuple val(meta), val(id) output: tuple val(meta), path("$id"), emit: sra path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n" """ eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')" if [[ ! -f "\${NCBI_SETTINGS}" ]]; then mkdir -p "\$(dirname "\${NCBI_SETTINGS}")" printf '${config}' > "\${NCBI_SETTINGS}" fi prefetch \\ $args \\ --progress \\ $id vdb-validate $id cat <<-END_VERSIONS > versions.yml "${task.process}": sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+') END_VERSIONS """ }