Dsl2/enhancement/sv sigs

[anoronh4]

Added 3 new processes:

• RunSVSignatures: using signature.tools.lib to run SV signatures
  • uses SV only
  • genome or exome (not sure if appropriate for exome mode)
• SomaticRunClusterSV: ClusterSV to assign SV to clusters and footprints
  • uses SV only
  • genome mode only
• SomaticRunSVclone: SVclone to assign SV and small mutations to individual clones
  • uses SV, SNPs, purity/ploidy (can be provided by Facets), bam file
  • genome mode only

Also updated HRDetect, which comes from the signature.tools.lib package as well. The version of signature.tools.lib is v2.1.2 for both processes now, so that they are expected to generate the same sv signatures. I also changed the name of the container folder, because now that the container services a process that is not HRDetect, the folder name hrdetect no longer fits. it is now called signaturetoolslib.

To-do:

• [x] Circos plot
• [x] Finalize SVclone output
• [x] Aggregate Outputs?
  • [x] Process1: bedpe
  • [x] Process2: clustering
  • [x] Process3: exposures, catalogues
  • [x] Process4: HRDetect
  • [x] Process5: SVclone
• [x] Separate SomaticRunSVclone to separate subworkflow due to maf requirement.

[gongyixiao]

And any cohort aggregation steps we need to add for these new modules?

[anoronh4]

And any cohort aggregation steps we need to add for these new modules?

That's a good point. An easy one would be to slap the SV signature results together and HRDetect results together in another file -- these are very simple text files.

[gongyixiao]

I have noticed that the result dir for svclone doesn’t have any files published although the job done successfully and there are results in the workdir. Please check either Francisco’s or Andrew’s run in my folder.

Also the sv_clustering result folder has an additional out/ subdir, which I think could be removed.