Add WTS support

[pdiakumis]

Adding datasharing support for the following (main) files output from the wts_tumor_only workflow:

wts_files <- dplyr::tribble(
    ~regex, ~type,
    "\\.bam$", "BAM_WTS_tumor",
    "\\.bam\\.bai$", "BAMi_WTS_tumor",
    "fusion_candidates\\.final$", "TSV_WTS_FusionCandidatesDragen",
    "quant\\.genes\\.sf$", "TSV_WTS_QuantificationGenes",
    "quant\\.sf", "TSV_WTS_Quantification",
  )
  wts_arriba_files <- dplyr::tribble(
    ~regex, ~type,
    "fusions\\.pdf$", "PDF_WTS_FusionsArriba",
    "fusions\\.tsv$", "TSV_WTS_FusionsArriba",
  )

You simply need to specify the new --wts argument on the CLI for WTS samples. For example:

datashare.R \
  --wts \
  --subject_id SBJ05560 \
  --library_id_tumor L2401254 \
  --csv_output urls.csv \
  --append

The rest of the options remain unchanged.

[ohofmann]

Amazing - thank you! I missed the request last week; the included files should be a good starting point for the WEHI folks.