common-workflow-lab galaxy issues

common-workflow-lab / galaxy

Fork of Galaxy (http://galaxyproject.org/) attempting to implement the CWL spec.

https://www.commonwl.org

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issues

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Importing a workflow with embedded tools fails if the latest CWL version is a development one

#147 nsoranzo opened 1 month ago
0
Support outputs_to_working_directory

#146 mvdbeek opened 1 year ago
0
UI for CWL workflow/tool execution

#145 mr-c opened 2 years ago
2
default values of "class: File" or "class: Directory" need persisting

#144 mr-c opened 2 years ago
1
Update Cwl interactor to target newer upload tool

#143 mvdbeek opened 2 years ago
0
Diagnosis of failing tests

#142 mvdbeek opened 2 years ago
0
TypeError: unhashable type: 'list'

#141 mr-c opened 2 years ago
2
Bump handsontable from 2.0.0 to 10.0.0 in /client

#140 dependabot[bot] closed 2 years ago
1
Bump tensorflow from 2.5.1 to 2.5.2 in /lib/galaxy/dependencies

#139 dependabot[bot] closed 2 years ago
1
Fix a bunch of Galaxy tests

#138 mvdbeek closed 2 years ago
2
Enhance the Python typing for the files we touch

#137 mr-c closed 2 years ago
10
[ImgBot] Optimize images

#136 imgbot[bot] closed 3 years ago
0
Better $(runtime) support

#135 mr-c opened 3 years ago
0
CI: report with CWL conformance test badges

#134 mr-c opened 3 years ago
0
Fix interactor to allow running tests without job definition

#133 mvdbeek closed 3 years ago
2
Add conformance CI, update and fix tests

#132 mvdbeek closed 3 years ago
1
Port ``when`` (conditonal) handling back into core + ga/format2

#131 jmchilton closed 1 year ago
1
More robust should_fail handling when running CWL conformance tests.

#130 jmchilton closed 3 years ago
0
[WIP] Update cwl rewrite tool

#129 mvdbeek closed 3 years ago
6
[WIP] Pass along ephemeral_collection.persistent_object

#128 mvdbeek closed 3 years ago
3
Fix workflow field input defaults.

#127 jmchilton closed 3 years ago
0
Figuring out path forward on complicated output sources

#126 jmchilton opened 3 years ago
8
Various fixes and enhancements

#125 jmchilton closed 3 years ago
0
Update CWL populator load conformance tests for $imports in CWL 1.2.

#124 jmchilton closed 3 years ago
1
[WIP] Implement conditionals.

#123 jmchilton closed 1 year ago
4
Tracking accomplishments at #BioHackEU20

#122 mr-c closed 3 years ago
1
Migrate Travis Tests to Github Actions

#121 jmchilton closed 3 years ago
2
Annotate CWL 1.2 Conformance Tests

#120 jmchilton closed 3 years ago
0
Fix object_store_store_by handling

#119 mvdbeek closed 3 years ago
1
Fix FieldTypeParameterValue wrapping

#118 mvdbeek closed 3 years ago
1
Parse creator and license information from CWL documents.

#117 jmchilton opened 4 years ago
1
Rework resource handling for cwltool>=3.0.20200317142916

#116 jmchilton closed 3 years ago
3
Update CWL Branch

#115 jmchilton closed 4 years ago
0
Bump jquery from 2.2.4 to 3.5.0 in /client

#114 dependabot[bot] closed 4 years ago
1
Re-visit library vs. Galaxy usage of UUIDs in tool loading.

#113 jmchilton opened 4 years ago
0
correct the dataset extension set problem

#112 hmenager closed 5 years ago
0
problem with workflows upload

#111 hmenager closed 5 years ago
1
problem handling failed jobs

#110 hmenager closed 5 years ago
1
correct a few module import paths that have changed

#109 hmenager closed 5 years ago
0
untested: relaxing the path checks

#108 mr-c closed 5 years ago
1
relax path checks

#107 mr-c closed 5 years ago
0
set CWL workflow name to label, not file path

#106 hmenager closed 5 years ago
0
allow to upload CWL workflows to Galaxy using the API

#105 hmenager closed 5 years ago
0
Fix some regressions

#104 hmenager closed 5 years ago
4
Documentation on CWL-in-Galaxy

#103 stain opened 5 years ago
1
[ImgBot] Optimize images

#102 imgbot[bot] closed 5 years ago
0
Refactor the hacky EphemeralCollection (inputs that are produced by expressions) in cwlbranch into something that can be included into Galaxy core.

#101 jmchilton opened 5 years ago
0
Implement workflow input expressions for core that CWL can leverage.

#100 jmchilton opened 5 years ago
0
Polish and enhance FieldType handling to get it into core.

#99 jmchilton opened 5 years ago
0
Refactor persistent file name tracking into core.

#98 jmchilton closed 5 years ago
1