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Commits on Jun 26, 2024

• Merge pull request #1088 from apaul7/vt-image-update

  apaul7

  committedJun 26, 2024
  5fda2d9

• update vt docker image

  

  Alex Paul

  committedJun 26, 2024
  90950db

Commits on Jun 21, 2023

• Merge pull request #1086 from tmooney/update_cwltool

  tmooney

  committedJun 21, 2023
  8da2b1c

• Update to cwltool==3.1.20230601100705

  tmooney

  committedJun 21, 2023
  3c948c9

• Use enums for inputs that are passed to enums.

  tmooney

  committedJun 21, 2023
  d3ca38a

Commits on Dec 27, 2022

• Merge pull request #1083 from susannasiebert/pvactools

  susannasiebert

  committedDec 27, 2022
  0d2f354

• Upgrade to version 3.1.1

  susannasiebert

  committedDec 27, 2022
  01efd59

Commits on Dec 12, 2022

• Merge pull request #1077 from johnegarza/fda_metrics_split_on_sequence

  johnegarza

  committedDec 12, 2022
  4bf4cb1

Commits on Dec 7, 2022

• Update parser to handle the latest updates to upstream scripts

  johnegarza

  committedDec 7, 2022
  b78224d

• updates from gchang to calculate metrics per file instead of per pair when fastqs are provided as input

  johnegarza

  committedDec 7, 2022
  369a072

Commits on Nov 22, 2022

• Cast possible ints to strings

  johnegarza

  committedNov 22, 2022
  27ff876

Commits on Nov 6, 2022

• Fix incorrect read count for aligned rna

  johnegarza

  committedNov 6, 2022
  8445be2

Commits on Nov 3, 2022

• Use aligned cram file and name when possible, since it's already provided as an output file

  johnegarza

  committedNov 3, 2022
  29d29bb

• Give output files unique names to ensure proper staging

  johnegarza

  committedNov 3, 2022
  fe443a7

Commits on Nov 2, 2022

• Merge pull request #1080 from tmooney/update_mapq0_filter_to_054

  tmooney

  committedNov 2, 2022
  a53dde2

• Update docker image to 0.5.4 for handling of case of 0-depth variant.

  tmooney

  committedNov 2, 2022
  6686eaa

Commits on Nov 1, 2022

• Script cleanup from gchang

  johnegarza

  committedNov 1, 2022
  03650ca

Commits on Sep 13, 2022

• Merge branch 'master' into fda_metrics_split_on_sequence

  johnegarza

  committedSep 13, 2022
  3bde367

• fix ordering for optional named params in python3

  johnegarza

  committedSep 13, 2022
  d38588b

• Merge pull request #1075 from johnegarza/fda_metrics_bugfixes

  johnegarza

  committedSep 13, 2022
  bcbe0dd

Commits on Sep 12, 2022

• Update output type in immuno.cwl

  johnegarza

  committedSep 12, 2022
  aa1d73a

• Fix scatter param

  johnegarza

  committedSep 12, 2022
  5b5034e

• Calculate stats per sequence

  johnegarza

  committedSep 12, 2022
  e3c3611

Commits on Aug 15, 2022

• Fix tool paths

  johnegarza

  committedAug 15, 2022
  f5c9a5a

• Better dup parser logic

  johnegarza

  committedAug 15, 2022
  4263639

Commits on Aug 10, 2022

• Merge pull request #1070 from johnegarza/immuno_FDA_metrics

  johnegarza

  committedAug 10, 2022
  b44862c

• Add inputs, outputs, and logic for summary table generation

  johnegarza

  committedAug 10, 2022
  411f137

• fastqc can't handle crams

  johnegarza

  committedAug 10, 2022
  94d6ae1

• fix file type

  johnegarza

  committedAug 10, 2022
  b186047

• Fix file extraction logic

  johnegarza

  committedAug 10, 2022
  4a98c03

• cromwell refuses to connect to internal registry

  johnegarza

  committedAug 10, 2022
  78b377e

• metrics tools bugfixes

  johnegarza

  committedAug 10, 2022
  2018f97

Commits on Aug 9, 2022

• Merge pull request #1073 from tmooney/upgrade_mapq0_filter_to_v0.5.3

  tmooney

  committedAug 9, 2022
  1548c42

• Upgrade mapq0 filter to v0.5.3

  tmooney

  committedAug 9, 2022
  c727de3

Commits on Jul 13, 2022

• Merge pull request #1072 from susannasiebert/pvactools

  susannasiebert

  committedJul 13, 2022
  31a179d

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