Implement a subset of the Common Workflow Language#12909

Draft

nsoranzo wants to merge 59 commits intogalaxyproject:devfrom common-workflow-lab:cwl-1.0

+3,422-324

Commits on Dec 5, 2024

[WIP] Implement records - heterogenous dataset collections.

jmchilton
authored and
nsoranzo
committed
Deal with workflow definitions without position fields.

jmchilton
authored and
nsoranzo
committed
Implement subset of the Common Workflow Language tool and workflow formats.

committed
CWL Testing and Runner Improvements.

jmchilton
authored and
nsoranzo
committed
Swap default for beta formats (do not include in Galaxy).

jmchilton
authored and
nsoranzo
committed
WIP: Work toward Galaxy-flavored CWL tools.

jmchilton
authored and
nsoranzo
committed
[WIP] Implement client UI for field parameter type for CWL.

jmchilton
authored and
nsoranzo
committed
WORKAROUND TO GET TAR TO DIRECTORY WORKING AGAIN.

jmchilton
authored and
nsoranzo
committed
Add fields parameter to create collection schema

mvdbeek
authored and
nsoranzo
committed
Fix non_data_connection workflows

mvdbeek
authored and
nsoranzo
committed
Fix handling of uploaded_file_name

mvdbeek
authored and
nsoranzo
committed
Fix directory location tests

mvdbeek
authored and
nsoranzo
committed
start documenting state of CWL support

mr-c
authored and
nsoranzo
committed
Add sentinel value workaround for GALAXY_SLOTS hack

mvdbeek
authored and
nsoranzo
committed
Assert length of input connections, instead of inputs when disconnecting steps

mvdbeek
authored and
nsoranzo
committed
Fix type hints

mr-c
authored and
nsoranzo
committed
Disable cheetah in configfiles, env vars for cwl tools

mvdbeek
authored and
nsoranzo
committed
Drop test_deserialize_cwl_tool, already testing that more accurately in cwl_test.py

mvdbeek
authored and
nsoranzo
committed
Fix wrong resolution of Any type when re-using CWL tools

mvdbeek
authored and
nsoranzo
committed
Coerce discovered optional files to data

mvdbeek
authored and
nsoranzo
committed
Fix complex types via record collection type

mvdbeek
authored and
nsoranzo
committed
Fix handle_known_output for nested output records

mvdbeek
authored and
nsoranzo
committed
Skip staging inputs for outputs

mvdbeek
authored and
nsoranzo
committed
Fix packed document support if main/#main is tool instead of workflow

mvdbeek
authored and
nsoranzo
committed
Fix tool-provided metadata for CONVERTER_tar_to_directory
nsoranzo
committed
Implement rough mapping between EDAM formats and datatypes

mvdbeek
authored and
nsoranzo
committed
Support uploading directory literals

mvdbeek
authored and
nsoranzo
committed
Keep directory parameters in job parameters

mvdbeek
authored and
nsoranzo
committed
Merge subworkflow input logic?

mvdbeek
authored and
nsoranzo
committed
Drop divergent to_cwl/from_cwl, factor out extra_step_state building

mvdbeek
authored and
nsoranzo
committed
TreeDict fix

mvdbeek
authored and
nsoranzo
committed
Use regular staging for CWL tests instead of allow_path_paste, which is broken

mvdbeek
authored and
nsoranzo
committed
Fix directory file upload request

mvdbeek
authored and
nsoranzo
committed
Record unnamed_outputs as job outputs, wait for job outputs in staging function

mvdbeek
authored and
nsoranzo
committed
Fix directory uploads

mvdbeek
authored and
nsoranzo
committed
Download complex outputs

mvdbeek
authored and
nsoranzo
committed
Download secondary files as well

mvdbeek
authored and
nsoranzo
committed
Implement downloading directory archive

mvdbeek
authored and
nsoranzo
committed
Quickfix for moving away tool working directory

mvdbeek
authored and
nsoranzo
committed
Various fixes for stricter cwltool and cwltest

mvdbeek
authored and
nsoranzo
committed
Fix up ontology to datatype mapping for __FETCH_DATA__

mvdbeek
authored and
nsoranzo
committed
Shortcut param_dict building for CWL tools

mvdbeek
authored and
nsoranzo
committed
WIP: untar directory to extra_files_path

mvdbeek
authored and
nsoranzo
committed
Add test for workflow default file overrides tool default file

mvdbeek
authored and
nsoranzo
committed
WIP:CWL default file value_from work

mvdbeek
authored and
nsoranzo
committed
Into split trans to app

mvdbeek
authored and
nsoranzo
committed
Separate and fix value_from overriding default

mvdbeek
authored and
nsoranzo
committed
Ensure that expression tool null values are treated as null values when replacing with default

mvdbeek
authored and
nsoranzo
committed
Hack: default files in FieldTypeToolParameter

mvdbeek
authored and
nsoranzo
committed
Fix literal value if field type

mvdbeek
authored and
nsoranzo
committed
Replace file location with URL ...

mvdbeek
authored and
nsoranzo
committed
Pack workflow

mvdbeek
authored and
nsoranzo
committed
Update list of new failing 1.2 tests

mvdbeek
authored and
nsoranzo
committed
Drop now passing red tests

mvdbeek
authored and
nsoranzo
committed
Exclude red and required 1.0 tests from github matrix

mvdbeek
authored and
nsoranzo
committed
Fix workflow cancellation exceptions

mvdbeek
authored and
nsoranzo
committed
Fix output addition to history if input name is same as output name

mvdbeek
authored and
nsoranzo
committed
Fix directory unpacking

mvdbeek
authored and
nsoranzo
committed
Fix test_composite_datatype_stage_upload1 test
nsoranzo
committed