Code

CWL Pipefish compatibility#4636

Code

Merged

DailyDreaming merged 24 commits intomasterDataBiosphere/toil:masterfrom issues/4633-cwl-pipefish-compatibilityDataBiosphere/toil:issues/4633-cwl-pipefish-compatibilityCopy head branch name to clipboardNov 9, 2023

+283-128

Commits

Commits on Oct 18, 2023

• Add a bunch of value resolving logging

  adamnovak

  committed
  23c7346

• Quiet debugging a bit

  adamnovak

  committed
  eb28215

• Move default setting for workflows so it works on subworkflows

  adamnovak

  committed
  f78f3b6

• Remember to keep making a ToilFsAccess on the leader

  adamnovak

  committed
  b21648e

• Satisfy MyPy

  adamnovak

  committed
  856e2d6

• Stop giving CWL containers directories full of broken symlinks

  adamnovak

  committed
  5ca06b6

Commits on Oct 19, 2023

• Merge remote-tracking branch 'origin/master' into issues/4633-cwl-pipefish-compatibility

  adamnovak

  committed
  385a627

• Update test to expect no symlinks

  adamnovak

  committed
  f1bf10c

• Move CWL integration tests for bioconda/biocontainers to integration test runs

  adamnovak

  committed
  2e2eff3

Commits on Oct 24, 2023

• Wrap mkdtemp to fix #4644

  adamnovak

  committed
  6fd95a3

• Sort imports in example scripts

  adamnovak

  committed
  78033df

• Use absolute-ized paths for work and coordination directories

  adamnovak

  committed
  23b1cc7

Commits on Oct 26, 2023

• Merge branch 'master' into issues/4633-cwl-pipefish-compatibility

  adamnovak

  authored
  716ad3c

Commits on Nov 2, 2023

• Merge remote-tracking branch 'upstream/master' into issues/4633-cwl-pipefish-compatibility

  adamnovak

  committed
  d941815

• Split CI run conditions into different rules

  adamnovak

  committed
  e0131f5

• Run the CWL integration tests on any branch that changes the CWL runner

  adamnovak

  committed
  ddf653b

• Ship CWL test logs as junit files as unbounded size so we can get the failures

  adamnovak

  committed
  cb14501

• Fix yaml

  adamnovak

  committed
  a322c92

• Add missing keys and close quotes

  adamnovak

  committed
  ac1c7a4

Commits on Nov 9, 2023

• Revert "cwl: use the latest commit from the proposed CWL v1.2.1 branch (#4565)"

  Show description for 1f2df97
  adamnovak

  committed
  1f2df97

• Run CWL tests if they themselves change

  adamnovak

  committed
  e3444bc

• Turn off bioconda/biocontainers tests since they fail a nontrivial amount of the time because something at the other end is broken

  adamnovak

  committed
  50d6cea

• Merge remote-tracking branch 'upstream/master' into issues/4633-cwl-pipefish-compatibility

  adamnovak

  committed
  f93d1c9

• Skip differently

  adamnovak

  committed
  04ce883