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2.4.0
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@arkal arkal released this 08 Mar 19:16
· 94 commits to master since this release
releases/2.4.0
05007c7

ProTECT 2.4.0 is here with so many goodies to share!

Major new features include:

  1. HG38 support: ProTECT now supports neoantigen prediction on samples using the GRCh38/HG38 reference genome. Like hg19, hg38 references are provided in our s3 bucket at s3://cgl-protect-data/hg38_references/
  2. Altered-self support: ProTECT now has measures to calculate the binding scores for the corresponding wild-type peptides for each neoepitope and then consider that while ranking the results.
  3. User-specified dockerized-tool versions: ProTECT now allows the user to specify the version of a tool to use in the analysis. This requires the user to ensure that the tag exists in the provided dockerhub.
  4. http, https and ftp download support: ProTECT can now pull samples and references from http, https and ftp endpoints.
  5. Support for non-standard naming scheme for fastqs: ProTECT now allows users to optionally specify a separate link for the _2.fastq files (and ignores the previous requirement of the two _1 and _2 files sharing a common naming schema and existing in the same directory). This functionality along with https support allows users to pull signed aws s3 links into their pipelines.
  6. Added code that produces Dockerised versions of ProTECT (Currently is hardcodes the version to be 3.2.0 but this will be addressed in #173)

Other minor features and bugfixes:

  1. Updated the flow chat, doc strings and all associated supporting material to more accurately describe ProTECT.
  2. Bumped Transgene to 2.0.0 (using the correct tag of the Docker image)
  3. Fixed rsem to correctly request disk space
  4. Bumped Toil dependency to 3.5.2 (Handles some issues seen in a 90-samples scale-run)
  5. Fixed a small bug where in certain cases star was asking for float disk requirements and causing Toil to crash.
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