The Nextflow pipelines currently have a finalize_output stage. This was intended to be used to compress the final output files. Output finalization may be platform specific and therefore should be handled by a script which runs after the pipeline succeeds. Remove the finalize_output stages from the nextflow pipelines and replace them publishDir directives within processes.
The Nextflow pipelines currently have a
finalize_outputstage. This was intended to be used to compress the final output files. Output finalization may be platform specific and therefore should be handled by a script which runs after the pipeline succeeds. Remove thefinalize_outputstages from the nextflow pipelines and replace thempublishDirdirectives within processes.