gbcms upgrade

• small fix to support new column from gbcms

Voyager

Release with changes for running within the MSK Voyager system

Changes are mostly related to upgrading scripts to python3, and restructuring the pipeline outputs

Specifically we are now using type: File[] instead of type: Directory so that we can register the bams in the Beagle DB.

1.3.40

• upgrade to Toil-MSK 3.21.0 (to fix ResolveIndirect bug)
• fix for tag_hotspots script (no longer has logic for parsing hgvsp_short)
• fix for remove_variants_by_annotation script (include MET splice_site variants)

1.3.38

New tag for a few fixes to get kickoff scripts working again

1.3.36

• remove stdout and stderr redirection for CNV jobs (easier to see logging in main log file)

Note: new setup.sh script no longer installs Rptashkin textplot R module, needs manual install

1.3.35

• fix Library_input and Library_yield columns in QC report
• deal with special characters in path to outputs (underlying cwltool issue here: common-workflow-language/cwltool#1260)
• fix removal of non-matching fastqs from title file in kickoff
• use Abra cores and memory as input parameters
• use consistent project_name field for MSI workflow in kickoff step
• split insert sizes and coverage distribution graphs by tumor and normal
• new method for writing version info to inputs files

1.3.28

fix for saving / reading version info into version.yaml

merge with DMP dmp_prod/master

Merged mainly to obtain fix in get_pos() function that prevents sample ID mismatches such as sample_1 matching to sample_11

config files consolidation

Merged run files / tools / params into one template file for each workflow.

Intended use is for these configs to be filled out after cloning the repo. Then installed using pip install .

picard tmpdir fix

• hard coded /scratch into ARRG / FX tools to prevent long runtimes (need to find better solution)