Code

Subsampler and augur workflow#483

Code

Merged

dpark01 merged 52 commits intomasterbroadinstitute/viral-pipelines:masterfrom subsampler-dpbroadinstitute/viral-pipelines:subsampler-dpCopy head branch name to clipboardSep 26, 2023

+392-39

Commits

Commits on Aug 22, 2023

• test subsampler

  schaluva

  committed
  a74b0bf

• set outputs

  schaluva

  committed
  b861b55

• point to right dir

  schaluva

  committed
  4299b4c

• add in all rule inputs

  schaluva

  committed
  388be77

• reset push to dockstore

  schaluva

  committed
  53839db

• hold output from opt/subsampler dir

  schaluva

  committed
  8b94ebe

• output /opt..

  schaluva

  committed
  c4b8671

• test

  schaluva

  committed
  3bd21bc

• check directory structues

  schaluva

  committed
  eb5124d

• original dir pwd

  schaluva

  committed
  744e8af

• figure out how to get to root

  schaluva

  committed
  f180d6f

• get back to cromwell root

  schaluva

  committed
  93ab0ae

• make copies of outputs in cromwell_root

  schaluva

  committed
  a13e4f9

Commits on Aug 23, 2023

• expand to more rules

  schaluva

  committed
  3563559

• add in subsampler

  schaluva

  committed
  6c7d1c6

• remvoe default values for dates

  schaluva

  committed
  a67b21f

• make start and end optional

  schaluva

  committed
  e31adcf

• fix rule name

  schaluva

  committed
  5bffdd4

Commits on Aug 24, 2023

• clean up and add subsample outputs to wf outputs

  schaluva

  committed
  e7f7347

Commits on Sep 8, 2023

• initial setup of subsampler->augur pipeline

  dpark01

  committed
  22feb4a

• wdl syntax fixes

  dpark01

  committed
  6289875

• fix subsample_by_casecounts output refs, add some extra outputs to augur_from_msa_with_subsampler

  dpark01

  committed
  f550d81

• remove genbank test from cromwell unit testing

  dpark01

  committed
  7933f21

• Merge branch 'master' into subsampler-dp

  dpark01

  authored
  6ba944c

• Merge branch 'master' into subsampler-dp

  dpark01

  authored
  8728b92

Commits on Sep 9, 2023

• Merge branch 'master' into subsampler-dp

  dpark01

  authored
  e6dbd51

Commits on Sep 10, 2023

• Merge branch 'master' into subsampler-dp

  dpark01

  authored
  8d65690

Commits on Sep 11, 2023

• bump nextstrain docker from 20211012T20 to 20230905T19

  dpark01

  committed
  dd3258a

• switch from xz to zst

  dpark01

  committed
  4d1ea6b

Commits on Sep 14, 2023

• refresh dockstore

  schaluva

  committed
  4cae41b

• refresh dockstore with PR not as draft

  schaluva

  committed
  024f6e8

• bump AUGUR_RECURSION_LIMIT to 100k

  dpark01

  committed
  95a961a

Commits on Sep 18, 2023

• more recursion limit on augur translate

  dpark01

  committed
  dd67453

Commits on Sep 19, 2023

• merge in nextstrain updates

  dpark01

  committed
  1c6112e

• fix delocalization

  dpark01

  committed
  21d1adc

Commits on Sep 20, 2023

• fix delocalization

  dpark01

  committed
  59f16e3

Commits on Sep 21, 2023

• make more subsampler inputs optional and add more typing to inputs

  dpark01

  committed
  cc1b737

• formatting

  dpark01

  committed
  fc5c2c7

• add counts to output and blank some default inputs

  dpark01

  committed
  a8926ff

Commits on Sep 22, 2023

• depart from snakemake and just run dag steps manually

  dpark01

  committed
  bcbd13e

• crank memory, add zstd support, fail fast

  dpark01

  committed
  27eb2b3

• update default compression of subsample output and add more file patterns to workflow inputs

  dpark01

  committed
  6d0520a

• bump hardware requests and add hardware utilization telemetry

  dpark01

  committed
  cb01dc0

• oops, bump to wdl 1 command bock

  dpark01

  committed
  54ec1ab

• add progress statements

  dpark01

  committed
  194082c

• work in execution platforms CWD instead of in /opt/subsampler which is often on a tiny hard OS disk

  dpark01

  committed
  59ad5d5

• expose ram as knob

  dpark01

  committed
  3f8c374

• absolute path to scripts

  dpark01

  committed
  ee01ab2

• fix the broken --keep function

  dpark01

  committed
  ef36163

Commits on Sep 25, 2023

• reshape vm defaults and subsampler default inputs

  dpark01

  committed
  3095833

• ram telemetry not working, revert to 30GB

  dpark01

  committed
  3345925

• lower default baseline again to 1e-4, fix spelling of start-date and end-date parameters

  dpark01

  committed
  0fba1bc