process BCLCONVERT { tag "$meta.id" label 'process_high' if (params.enable_conda) { exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers." } container "nfcore/bclconvert:3.10.5" input: tuple val(meta), path(samplesheet), path(run_dir) output: tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,optional:true ,emit: undetermined tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx tuple val(meta), path("Reports") ,emit: reports tuple val(meta), path("Logs") ,emit: logs tuple val(meta), path("**.bin") ,emit: interop path("versions.yml") ,emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ bcl-convert \\ $args \\ --output-directory . \\ --bcl-input-directory ${run_dir} \\ --sample-sheet ${samplesheet} \\ --bcl-num-parallel-tiles ${task.cpus} cat <<-END_VERSIONS > versions.yml "${task.process}": bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //') END_VERSIONS """ }