common-workflow-language/cwltool

Issues

• flaky conformance test with `cwltool`: simple_simple_scatter

  #2003 opened a month ago by mr-c
  0

• Running cwltool with empty inputs_object fails without a meaningful error message

  #2043 opened 2 months ago by WhiteGobo
  0

• We cannot pass an array of integers as a command line argument.

  #2034 opened 2 months ago by yamaken37
  3

• Selected input parameter type is not propagated as output parameter type

  #2039 opened 2 months ago by adrabent
  0

• Input `format` expression not considering `$namespaces`

  #2033 opened 3 months ago by fmigneault
  2

• `cwltool` Freezes When Not Using Inputs in Scatter Parallelization

  #2031 opened 3 months ago by gen740
  0

• `cwltool --print-dot` fails with python 3.8 (or newer) due pydot version 3.0.0 (or newer)

  #2027 opened 4 months ago by jmfernandez
  0

• dev docs: how to run the conformance tests with `pytest`

  #2023 opened 4 months ago by mr-c
  0

• Workflows with `DockerRequirement` fail when using Podman 5.0.2

  #2001 opened 4 months ago by tom-tan
  1

• Confusing provenance model (`wasStartedBy`/`qualifiedStart`/`wasEndedBy`/`qualifiedEnd`)

  #2007 opened 6 months ago by avillar
  0

• location url not executed correctly with --cachedir CACHE

  #1842 opened 2 years ago by jjkoehorst
  2

• --debug should print the URL of the downloading schema

  #2000 opened 6 months ago by inutano
  0

• Evaluation expressions that timeout can raise JSONDecodeError

  #1999 opened 6 months ago by brettcs
  0

• CWL Conditionals, when component doesn't handle condition when tool input parameter is a non-optional file with loadContents set to true

  #1969 opened 10 months ago by alexiswl
  2

• Add CITATION.cff / codemeta.json file

  #1967 opened 10 months ago by mr-c
  0

• Calling cwltool.main() with preparsed args and provenance fails unless unparsed args are also provided

  #1963 opened 10 months ago by davidjsherman
  4

• cwltool hangs running fast jobs in Podman

  #1961 opened a year ago by kuanyili
  2

• switch from setuptools to hatchling?

  #1935 opened a year ago by mr-c
  1

• installing for regular users: use pipx

  #1946 opened a year ago by mr-c
  0

• cwltool --validate is success --make-template becomes failure

  #1944 opened a year ago by manabuishii
  0

• ``cwltool --pack`` does not handle collisions correctly

  #1937 opened a year ago by mvdbeek
  2

• stop supporting Python 3.7

  #1871 opened a year ago by mr-c
  1

• wildcard glob failing to be collected in tmp directory for hhsearch program using cwltool

  #1928 opened a year ago by DanBuchan
  2

• bind source path does not exist - cwltool keeps waiting / running does not stop

  #1887 opened a year ago by jjkoehorst
  2

• error if input is named `id`

  #1922 opened a year ago by mr-c
  0

• shutil.rmtree fails in M2 mac

  #1913 opened a year ago by naga-onu
  3

• How to set the number of parallels when using scatter

  #1827 opened 2 years ago by kongxiangya
  5

• cwltool does not properly detect available podman containers

  #1884 opened a year ago by jmfernandez
  1

• regression of cwltool performance by 5-7 minutes around 1st of june

  #1916 opened a year ago by azat-badretdin
  9

• cwltool throws an error when `secondaryFile`s are specified as a list in a workflow and as a single element in a tool

  #1912 opened a year ago by ThomasHickman
  0

• Schema salad error validating CWL enum definitions

  #1908 opened a year ago by fmigneault
  2

• Cannot load CWL definition directly with Python objects using `Factory` class

  #1903 opened a year ago by fmigneault
  0

• if the user's tmp drive is full, provide a better error message

  #1899 opened a year ago by mr-c
  0

• Deadlock with podman (at least 4.5.0) and simple workflow

  #1883 opened a year ago by jmfernandez
  0

• Provenance capture of all information in input yaml file

  #1889 opened a year ago by jjkoehorst
  0

• cached cannot handle URLs as input files

  #1888 opened a year ago by jjkoehorst
  1

• Download progress from input files through yaml

  #1886 opened a year ago by jjkoehorst
  0

• CWLProv: no trace of secondaryFiles for workflow activity

  #1879 opened a year ago by simleo
  0

• cwltool 4.0.0: defined public APIs, semver versioning

  #1875 opened a year ago by mr-c
  0

• cwltool --validate should error on jshint errors and certain warnings

  #1874 opened a year ago by tetron
  0

• cwltool --validate doesn't check for InlineJavascriptRequirement when it should

  #1873 opened a year ago by sjaenick
  1

• Required secondaryFiles outputs do not work in CWL CommandLineTools which run in Docker

  #1869 opened a year ago by ThomasHickman
  4

• `--tmpdir-prefix` argument not checked for trailing delimiter

  #1860 opened a year ago by sjaenick
  0

• cwltool exits with a 0 code even when an error occurred

  #1855 opened a year ago by fbacall
  1

• Executing workflow from argument file with provenance not working as expected

  #1843 opened 2 years ago by jjkoehorst
  0

• temp dir not respected with http retrieval

  #1841 opened 2 years ago by jjkoehorst
  0

• add "cwltool:outdir" support for input YAML

  #1837 opened 2 years ago by mr-c
  0

• [copy file] Issue in copying file in specific directory

  #1834 opened 2 years ago by linsherpa
  1

• very small numbers get turned into scientific notation on the command line

  #1831 opened 2 years ago by mr-c
  0

• Workflow error with HTTP files and --cachedir

  #1828 opened 2 years ago by bartns
  0