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Twist_Solid v0.10.0
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@github-actions github-actions released this 01 Dec 13:12
v0.10.0
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Main new features in v0.10.0

  • Scripts, configs and documentation for downloading all reference files used by the pipeline
  • Restructuring of the pipeline config files

Reference download

All files used by the pipeline can now be downloaded us the hydra-genetics command line tool.

Config restructuring

The config folder has now sub folders to avoid file cluttering.
The main config files have been split up into two configs, one for data files and one for software settings. The file paths in the data config are generalized so that only three different variables are needed to be adjusted, especially if the reference files are downloaded with the reference download tool.

TERT

2 new TERT promoter positions have been granted hotspot status

Fuseq-WES

Filtering of artifact fusion pairs can now be specified in a text file specified in the config.

RNA fusion report

Filtering of false positive fusions and cut-off values are now configurable (for Star-fusion and FusionCatcher) using a text file specified in config. Increased the list of fusions that are filtered from previous release based on more analysed samples.

Features

  • 2 new TERT positions added to report (3617acb)
  • add blacklist for fuseq_wes filtering (6bc03e3)
  • make fusion filtering configurable and add more fp fusions (5ed5c97)
  • more conda updates (df2b77c)
  • report internal callers for fusioncatcher (d5fccad)
  • setup files for reference file validation and fetching using yaml files (7078c04)
  • singularity build script update (8a8b665)
  • update to latest files used by config (07e351c)
  • update to newer hotspot file and clean config (72ef4ff)
  • use v0.1.0 of fusion module to filter FP Fuseq_WES calls (3c30fb1)

Bug Fixes

  • add lambda to functions so that they are only valuated when used (0b85dda)
  • add missing extra option in star-fusion (7476a0d)
  • add missing type (35e5f6e)
  • change from svdb_query file to svdb_merge file (1ed29ad)
  • configs for reference profile (6262775)
  • correct path in config (dd63afa)
  • handle reference creation with unit file containing both T and N (61b7764)
  • increased star_fusions wall time (5ff15de)
  • lamda in correct position (128aa8f)
  • minor config updates (8296226)
  • new rna fusion filter file without duplicate entry and header (280fd4a)
  • pycodestyle (36eed32)
  • support header with fusions filtering (c8a8bb7)
  • updarw config files to match current setup (0e689db)
  • update configs and restructure (7f397de)

Documentation

  • update documentation (0fd09ea)
  • update reference page with instructions to download reference files (3abac1f)
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