Output the files that are used for the final report

[ashotmarg]

Is your feature related to a problem?

The final report provides a nice summary of the run, however it would be great to have all those files that the report is based on (e.g., "itr_coverage_trimmed.tsv") explicitly output along with the report. This way, users will have the option to e.g., plot with their tools and/or process the files according to their needs. As of now, these files (e.g., the "itr_coverage_trimmed.tsv") are only used in the channels.

Describe the solution you'd like

A simple solution would be to provide a publishDir directive for the relevant processes. E.g., like this:

publishDir (
        params.out_dir,
        mode: "copy"
    )

Describe alternatives you've considered

The solution above worked for me for the "itr_coverage_trimmed.tsv" file I was interested in but I guess all such similar files (used for the report) could be output in a dedicated folder (e.g., called report_files or something like that ) inside the --out_dir.

Additional context

No response

[nrhorner]

Hi @ashotmarg

Thanks for your feature request! We'll review it for addition into the workflow.

[ashotmarg]

Thanks for the feedback @nrhorner .