Release 21.12.1

New Features

• Added default ram and cores for the pipeline

What's Changed

• Add ram and cores min by @nikhil in #123
• Release 12.12.1 by @nikhil in #124

Full Changelog: 21.12.0...21.13.0

Release 21.12.0

Features

• Fixed handling of empty mafs files (#122)
• Prevent gcms from failing from empty vcfs (#122)

Release 21.11.0

Features

• Handle empty maf in maf2vcf (#121)

21.10.0

• Better handling of facets failures

Release 21.9.9

• Corrected data_sv and meta_sv file names

Release 21.9.8

• Added fillout workflow notes
• Added portal sv files to the output

Version 21.9.7

• update fillout workflow (samples_fillout_index_batch_workflow.cwl) to support input samples that do not have a .maf file but have a .bam file
• add tests/datasets.py to repo instead of using it from the pluto submodule
• refactor of test case import methods
• rename all run.sh files so that they more clearly convey which CWL task they are associated with

Version 21.9.6

• update fillout workflow (samples_fillout_index_batch_workflow.cwl) for singleton handling (single-sample sample-groups)

Version 21.9.5

• change TMB score calculation to use cBioPortal filtered maf

(NOTE: old TMB scores can be seen on bbdc928 https://github.com/mskcc/pluto-cwl/blob/bbdc928cf85db7d547170b1dae6074c8455d71c9/tests/test_tmb_workflow_cwl.py#L472-L496

new values can be seen here; https://github.com/mskcc/pluto-cwl/blob/b7220f1dda6cfabad3a0c43558493f9821e8fed3/tests/test_tmb_workflow_cwl.py#L472-L495)

Version 21.9.4

• added .tsv output files for MSI and TMB workflows