Code

Develop#13

Code

Merged

gconcepcion merged 68 commits intomainPacificBiosciences/HiFi-human-assembly-WDL:mainfrom developPacificBiosciences/HiFi-human-assembly-WDL:developCopy head branch name to clipboardNov 28, 2023

+1,335-397

Commits

Commits on May 20, 2023

• Added version print statements to all tasks.

  Show description for edee46d
  williamrowell

  committed
  edee46d

• CommandShellCheck, SC2046 Quote this to prevent word splitting.

  williamrowell

  committed
  74d14fa

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  bc86fa6

• Fix htsbox version command.

  williamrowell

  committed
  c631102

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  28d0011

Commits on May 24, 2023

• update submodule

  williamrowell

  committed
  052365f

Commits on Jun 2, 2023

• Create LICENSE

  williamrowell

  authored
  fcbd54c

Commits on Jun 6, 2023

• Set max retries to 3 for HPC backend configuration

  hkeward

  committed
  de2e218

Commits on Jun 27, 2023

• Format docs; add backend-specific docs

  hkeward

  committed
  0ba71f4

• Update paths for AWS reference files

  hkeward

  committed
  e1b4074

Commits on Jul 4, 2023

• Allow user to override container registry

  hkeward

  committed
  c7714fe

Commits on Aug 11, 2023

• Avoid underestimating disk size based on first element of array.

  williamrowell

  committed
  5d1299b

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  cb9f17f

Commits on Aug 14, 2023

• Merge pull request #7 from PacificBiosciences/bugfix/disk-size-arrays

  Show description for 6ea580a
  williamrowell

  authored
  6ea580a

Commits on Aug 16, 2023

• Calculate total bases input for each parent to set yak params on the fly

  gconcepcion

  committed
  9c6c96e

• less than not greater than

  gconcepcion

  committed
  c9f7092

Commits on Aug 23, 2023

• Document submitting the workflow directly to Cromwell using cURL

  hkeward

  committed
  e873f20

• Add dependencies.zip to gitignore

  hkeward

  committed
  902f926

• Merge pull request #8 from PacificBiosciences/docs/cromwell-curl-command

  Show description for f1e76ea
  hkeward

  authored
  f1e76ea

Commits on Sep 22, 2023

• Adding multi-reference alignment option

  gconcepcion

  committed
  56833d4

• add yak bloom filter condition

  gconcepcion

  committed
  a40d2a2

• fix coverage

  gconcepcion

  committed
  fcf9ffe

Commits on Sep 25, 2023

• determine yak settings for both parents rather than independently

  gconcepcion

  committed
  d462924

• fix tests and remove some debug comments I missed

  gconcepcion

  committed
  af88a08

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  137d6a9

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  6c02327

Commits on Sep 28, 2023

• Take a stab at estimating depth based on filesize.

  Show description for 49acf5c
  williamrowell

  committed
  49acf5c

• changed flag name and fixed my flipped logic

  williamrowell

  committed
  f24e1e6

• Adjusted tests.

  williamrowell

  committed
  42d0d84

• Memory is an int.

  williamrowell

  committed
  c8a9b8d

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  4273515

• added warning comment about estimating depth by filesize

  williamrowell

  committed
  2dc2760

Commits on Sep 29, 2023

• Explicitly pass default yak count and hifiasm params.

  williamrowell

  committed
  ebe6afe

Commits on Oct 2, 2023

• Merge pull request #10 from PacificBiosciences/wrowell/yak-suggestions

  Show description for eee833f
  gconcepcion

  authored
  eee833f

Commits on Oct 26, 2023

• update README to reflect array of reference inputs as well as arrays of aligned bam outputs

  gconcepcion

  committed
  05312fe

• Merge pull request #9 from PacificBiosciences/gconcepcion/yak-changes

  Show description for de41388
  gconcepcion

  authored
  de41388

• disclaimer and dockstore.yml

  gconcepcion

  committed
  8a84fa6

• Merge branch 'develop' into feature/print_versions

  gconcepcion

  authored
  8cf587a

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  894094f

• clean up README

  gconcepcion

  committed
  b9f0bca

Commits on Oct 27, 2023

• Merge pull request #6 from PacificBiosciences/feature/print_versions

  williamrowell

  authored
  8853083

Commits on Oct 31, 2023

• update input jsons

  gconcepcion

  committed
  461a6f8

Commits on Nov 1, 2023

• add -L3.1g for NGx calculation default for human genomes

  gconcepcion

  committed
  8a90cd3

Commits on Nov 3, 2023

• substitute paftools for htsbox

  gconcepcion

  committed
  deba05b

• clean up comments

  gconcepcion

  committed
  8b9a61d

Commits on Nov 7, 2023

• now that we are aligning haps separately, there is a single assembly input instead of a list

  gconcepcion

  committed
  150b4a4

Commits on Nov 15, 2023

• add double quotes and fix tests

  gconcepcion

  committed
  58bdf47

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  de6bf21

• update wdl-ci json

  gconcepcion

  committed
  cc5afcb

• update wdl-common

  gconcepcion

  committed
  fe8b97f

• update tests for new wdl-common

  gconcepcion

  committed
  b5b121e

• fix tests

  gconcepcion

  committed
  f2b175f

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  2471441

Commits on Nov 16, 2023

• attempt to fix tests

  gconcepcion

  committed
  c434e7d

• update test locaton and remove tests from non-humanassembly tasks

  gconcepcion

  committed
  979ab48

Commits on Nov 17, 2023

• update wdl config to reflect local HPC test running

  gconcepcion

  committed
  22c3fc2

Commits on Nov 20, 2023

• temporarily disable tests while troubleshooting

  gconcepcion

  committed
  421fcc7

• fix tests for CoA

  gconcepcion

  committed
  013c77f

• finally fixed?

  gconcepcion

  committed
  51a53aa

Commits on Nov 21, 2023

• Use latest version of wdl-ci

  hkeward

  committed
  d1b2510

• do not save haplotype bams and output trio merged bam

  gconcepcion

  committed
  a88f0c2

• update wdl-ci config file after successful tests

  github-actions[bot]

  committed
  37b6ffb

Commits on Nov 27, 2023

• shorten chm13 name

  gconcepcion

  committed
  24cfc8d

• update backends documentation

  gconcepcion

  committed
  cdcbc59

Commits on Nov 28, 2023

• variant calling for trio asm

  gconcepcion

  committed
  12c7f42

• cleanup README

  gconcepcion

  committed
  389d8ff

• paftools print version and minor doc fixes before merge

  gconcepcion

  committed
  13ef8d7

• ...

  gconcepcion

  committed
  b87d85b