DSL2: Make publication of large intermediate files opt-in

[scarlhoff]

On March 31st, we decided to make the publication of all large output files that are used for down-stream processing, particularly bam files after mapping, etc., opt-in.

[TCLamnidis]

The default output should only include BAMs for the following levels:

• Deduplication output
• Sample-level BAM (which goes in the final_bams dir)
• (optional) Genotyping bams, if different from sample-level ones.

Opt-in processes (e.g. MAPDAMAGE_RESCALING) do not need opt-in to publish, since they are themselves opt-in.

Had a quick look through modules.config. I believe these are some pending changes for this:

• SAMTOOLS_LENGTH_FILTER_INDEX|SAMTOOLS_FILTER_INDEX published indexes without checking params.bamfiltering_savefilteredbams
• SAMTOOLS_{SORT,INDEX}_MERGE_LANES needs option to opt-in for keeping the lanemerged bams.