This release of ProTECT targeted a couple of features 1. Issue 90 fixed a bug that wrote the results from all samples in the run to the same list of files in the output directory. Files are now written to their own individual directories under the output directory. 2. issue 83 added a little more description to the manual regarding s3am 3. Issues 85 added overwrite support for uploads to s3 4. Issue 95 fixed a log error where --max-cores-per-job was being grouped with the argument group used to specify whether the user wants to generate a config, or run ProTECT. 5. Issue 97 reduced the memory requested by STAR to keep it under 50G for a full genome run.
2.2.0
ProTECT 2.2.0 brings in the fifth SNV caller in the pipeline, Strelka, closing issue 73 . SNVs are accepted for downstream processing if a mutation is called by any 2 of the 5 callers.... for now. Issue 82 will be addressed in the future and will use more sophisticated machine learning approaches to get a consensus call.
2.1.5
This release featured 1. A fix to the `--max-cores-per-job` command line flag, removing it from the mutually exclusive group concerning creating a config file, or running ProTECT. 2. A slight tweak to the memory used by STAR, allowing for a sub-50G run with whole genome indexes.
2.1.4
Added a small section to the manual talking about the version of s3am we prefer.
2.1.3
Added the input parameters file to the pip distribution so `ProTECT --generate_config` will run as expected from pip-installed ProTECT
2.1.2
This release features a minor patch to the dynamic promise requests that fixes the "could not parse value" Error seen reported in BD2KGenomics/toil/issues/1063