v3.0.0-alpha1

This is a pre-release workflow. Please do not depend on this for production analysis.

This release is not supported by the PacBio Tech Support or Field Support teams. Please only use this if you are already in contact with PacBio R&D and providing active feedback on performance and results.

What's Changed

• Replaced pbsv with Sawfish v0.12.7 for structural variant calling. #175 #147
• Update to DeepVariant from v1.6.0 to v1.8.0. Removed deepvariant_version and custom_deepvariant_model_tar input options. #186
• Update CoLoRSdb from v1.1.0 to v1.2.0 #190
  • Note: The new CoLoRSdb files have been uploaded to AWS, Azure, GCP, and Zenodo, but the ref_map and tertiary_map files have not been updated. You will need to generate new map files and update your inputs.json templates to use the new CoLoRSdb release.
• Refactored write_ped_phrank task to move pedigree creation to native WDL functions. Added internal Array[Boolean] is_duo_kid and Array[Boolean] is_trio_kid for future tertiary analysis tools. #188

Full Changelog: v2.1.1...v3.0.0-alpha1

v2.1.1

What's Changed

Tool version updates:

• TRGT v1.5.1
• pb-cpg-tools v3.0.0
• StarPhase v1.1.0
• Paraphase v3.2.1

Full Changelog: v2.1.0...v2.1.1

v2.1.0

What's Changed

• Support input BAMs without basemods. Reads without basemods will not contribute to basemod pileups.
• Support input BAMs without rq tags. rq will not be calculated for these reads, but the reads will be aligned for downstream processes.

• Updated to TRGT v1.4.1. by @williamrowell in #173
  • Increased memory for trgt task to better support larger catalogs with lower complexity motifs.
  • Added the max_depth parameter and limited to 50 to reduce memory usage for high depth low complexity loci.
  • Reduced the number of samtools sort threads to lower total memory used for sort.
• Update to pbmm2 v1.16.99 prerelease. by @williamrowell in #177 Fixes behavior where SA tags were not stripped from aligned input.

• Remove StarPhase outputs that are not allowed as PharmCAT input (PharmGKB/PharmCAT/issues/204)
  • NO_READS is used in StarPhase output to indicate no-calls.
  • NO_MATCH is used when StarPhase can't match the variants to a known allele.
  • This workaround removes NO_READS/NO_MATCH outputs.

• Gracefully handle low depth samples with StarPhase/PharmCAT by @williamrowell in #176

Full Changelog: v2.0.7...v2.1.0

v2.0.7

Thanks for bearing with us through the last few releases as we addressed issues affecting specific backends and combinations of inputs. We should start to see more stability now.

What's Changed

• Testing: Added unit tests for all tasks (except read_pbsv_splits) using DNAstack/wdl-ci #157
• Fix: write_ped_phrank bug affecting singleton.wdl entrypoint in Cromwell.

Full Changelog: v2.0.6...v2.0.7

v2.0.6

This is a bugfix release.

What's Changed

• Revert SC1117 fixes that caused issues with miniwdl. by @williamrowell in #169

Full Changelog: v2.0.5...v2.0.6

v2.0.5

This patch primarily addresses an issue with provisioning write_ped_phrank on GCP and Terra.

• cleaned up documentation
• cleaned up input templates
• addressed shellcheck issues for several command calls

Full Changelog: v2.0.4...v2.0.5

v2.0.4

What's Changed

This release addresses an issue with how the workflow_version output string was generated. This was not detected by linting tools and only caused issues at runtime on Cromwell.

• v2.0.4 by @williamrowell in #156

Full Changelog: v2.0.3...v2.0.4

v2.0.3

What's Changed

• a change to write_ped_phrank (for wdlTools/DNAnexus compatibility) in v2.0.2 broke Cromwell compatibility; this has been fixed
• a change to pbsv_call (for miniwdl compatibility) in v2.0.2 broke wdlTools/DNAnexus compatibility; this has been fixed
• @informationsea fixed a typo in the stats output
• wiki submodule was removed, docs are in docs subdirectory

Full Changelog: v2.0.2...v2.0.3

v2.0.2

What's Changed

• Fix json2ped.py by @williamrowell in #153

Full Changelog: v2.0.1...v2.0.2

v1.2.1

Updated json2ped.py to handle missing sample sex input. 3d62f62

Note: The v1 branch will not receive new features.

Clone this branch with:

git clone \
  --depth 1 --branch v1.2.1 \
  --recursive \
  https://github.com/PacificBiosciences/HiFi-human-WGS-WDL.git

Full Changelog: v1.2.0...v1.2.1