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Commits on Sep 20, 2024

• add deprecation warning to README.md

  tomkinsc

  authored
  c9914e0

• Update README.md

  Show description for d3c3cb9
  tomkinsc

  authored
  d3c3cb9

Commits on Mar 27, 2020

• ensure read_structure override works for CheckIlluminaDirectory (#1007)

  Show description for e144969
  tomkinsc

  authored
  e144969

Commits on Mar 20, 2020

• bump cromwell/womtool/dxWDL/dx-toolkit versions (#1006)

  Show description for e758b89
  tomkinsc

  authored
  e758b89

Commits on Feb 14, 2020

• Update read_utils.py (#1005)

  Show description for 23de91e
  tomkinsc

  authored
  23de91e

• update source url for obtaining gatk 3.8 (#1003)

  Show description for 8f4dc6c
  tomkinsc

  authored
  8f4dc6c

Commits on Dec 9, 2019

• jinja2 case

  tomkinsc

  committed
  49579c5

Commits on Dec 3, 2019

• remove py2 (#999)

  Show description for a0a717d
  tomkinsc

  authored
  a0a717d

Commits on Oct 29, 2019

• handle when gatk jar is in subdir (#997)

  Show description for fb170d6
  tomkinsc

  authored
  fb170d6

Commits on Oct 19, 2019

• pin snakemake to 5.6.0 (#996)

  Show description for a98a8ea
  tomkinsc

  authored
  a98a8ea

Commits on Oct 18, 2019

• Merge pull request #995 from broadinstitute/dp-dxwdl

  Show description for 3282979
  dpark01

  authored
  3282979

• comment out *all* parameter_meta for now

  dpark01

  committed
  19dab54

• bugfix: never assume same filesystem! always use shutil.copyfile instead of os.rename

  dpark01

  committed
  ec03092

• fix krona tool version mismatch between tool/krona.py and requirements.txt

  dpark01

  committed
  812c56f

• revert to v2 instance, comment out all streaming parameter_meta for now in kraken

  dpark01

  committed
  85f3a1a

Commits on Oct 17, 2019

• try and see what happens if we revert to v1 instance for kraken

  dpark01

  committed
  5f6188a

Commits on Oct 16, 2019

• Merge pull request #994 from broadinstitute/dp-dxwdl

  Show description for 83a5fab
  dpark01

  authored
  83a5fab

• speling

  dpark01

  committed
  a7c3595

• update demux_launcher to use new stage numbering from dxWDL

  dpark01

  committed
  055e1b0

• stage numbering a little funny now

  dpark01

  committed
  cbe3dc6

• upgrade dx-toolkit 0.285 to 0.288

  dpark01

  committed
  d651b9e

• fix demux_plus dx defaults based on new numbering scheme

  dpark01

  committed
  49f7320

• looks like the new dxwdl gets rid of the common applet in simple linear dags?

  dpark01

  committed
  9306b9e

• cant assign glob to Array[File]+ so change to Array[File]

  dpark01

  committed
  8fdd5cf

• debug genbank workflow

  dpark01

  committed
  584bfec

• dxwdl 1.33 to v1.33

  dpark01

  committed
  f02b507

• upgrade dx_instance_types to v2

  dpark01

  committed
  92304ab

• update to cromwell 47 and dxWDL 1.33

  dpark01

  committed
  1e5be53

Commits on Oct 3, 2019

• picard 2.20.5 -> 2.21.1 (#991)

  tomkinsc

  authored
  9f5b2c0

• pin attrs=19.1.0 for now (#990)

  Show description for 7d972d6
  tomkinsc

  authored
  7d972d6

Commits on Sep 20, 2019

• update rundocker.sh (#986)

  Show description for 2eba604
  tomkinsc

  authored
  2eba604

• mention where to find latest version of viral-ngs on DNAnexus (#988)

  tomkinsc

  authored
  4dc6f82

• docs: more generic dsub example (#987)

  tomkinsc

  authored
  e741b2b

Commits on Sep 11, 2019

• conda config --set anaconda_upload no (#982)

  Show description for 02bdd51
  tomkinsc

  authored
  02bdd51

• update picard 2.18.11 -> 2.20.3 (#977)

  Show description for 1dd180d
  tomkinsc

  authored
  1dd180d

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