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@gongyixiao gongyixiao released this 07 May 23:50
· 579 commits to master since this release
1.3
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Learn about vigilant mode.
  1. Move delly output from MergeDellyManta to DellyCall #753
  2. Change --aggregate <tsv> format and logic to support aggregate of different cohorts in one run #755
  3. Change maximum run time to 500 hours for 3rd and 4th time of task retry so that jobs won't fail because of run time on JUNO #759
  4. Add hidden feature of supporting watch mode for --maping/--bamMapping <tsv>, --pairing <tsv> and --aggregate <tsv> #754 #755 . (No docs for how to use it. Only aiming for supporting routine operation in CCS. For questions please reach out to @gongyixiao @anoronh4 )
  5. move RunNeoantigen before SomaticFacetsAnnotation #764
  6. Feature/facets suite2.0 #762
  7. Fixed Facets armlevel file path for aggregate and when aggregation from existing results folder, duplicated normal alfred files were input into QcBamAggregate process #766
  8. Fixed SomaticCombineChannel process failure due to no read counts reporeted by Strelka2 when using it to call multiallelic #768
  9. Supports for multiple part of fastq files for the same lane as SampleX_L001_R1_001.fastq.gz and SampleX_L001_R1_002.fastq.gz #770
  10. Bugfix/use facets1 gene level amp filter #772
  11. improve splitLanes #774 (Increased Nextflow version requirement to 20.01.0)
  12. initialize pairingQc variable and set pairingQc to true when --QC par… #780
  13. fix facets seed random error #782
  14. fixed bam truncation bug by using beforeScript and catch_USR2 #767
  15. PR #790. Temporary solution for #777 and #785. Explain in the doc for #781
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