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Michael R. Crusoe mr-c

Common Workflow Language co-founder & Project Lead

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common-workflow-language/common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Python 1.1k 170
common-workflow-language/cwltool

Common Workflow Language reference implementation

Python 209 154
common-workflow-language/schema_salad

Semantic Annotations for Linked Avro Data

Python 40 33
shouldacite

Should you cite this software?

CSS 20 2
common-workflow-language/cwlprov

Profile for provenance research object of a CWL workflow run

10 1

1,994 contributions in the last year

Activity overview

Contributed to common-workflow-language/cwltool, common-workflow-language/schema_salad, simd-everywhere/simde and 5 other repositories

Contribution activity

July 2020

mr-c/safestringlib C Jul 9
mr-c/bwa-mem2 C++ Jul 9

Created a pull request in common-workflow-language/cwltool that received 1 comment

fix for https://github.com/DataBiosphere/toil/issues/3107

+8 −6 • 1 comment

require v1.2.0-dev4 conformance tests to pass Jul 7
add format test to CI & fix pydocstyle check Jul 7
Add link to CWL forum in the GitHub new issues screen Jul 3
Rename primary branch to main Jul 2
enable pytest 5.x and pytest-xdist >= 1.28 Jul 1

Loadcontents Jul 2
Test mixed workflow / tool versions. Jul 2
Docs/clarify schemadef Jul 2

don't throw out user provided flags Jul 9
Fix version to be correct Jul 9

Link to the CWL user guide recommended practices Jul 8
simplify parameter expressions Jul 3

master -> main Jul 2
enable pytest 5.x Jul 1

don't throw out user provided flags Jul 9

upgrade cwltool to cwl v1.2.0-dev4 Jul 7

Add link to CWL forum in the GitHub new issues screen Jul 3

cwlviewer like dot Jul 7
Kill Docker container if --cidfile is specified Jul 7
Content loading Jul 6
test_udocker: Fallback if psutil.tests is missing Jul 2
Re-add conda instructions Jul 2
Update README.rst Jul 2
Fix string interpolation and backslash escaping to match 1.2 spec. Jul 2
Don't map file to local filesystem if the scheme is not file:// Jul 1

Add section about packed documents. Jul 6
Loadcontents Jul 6
Test mixed workflow / tool versions. Jul 2
Test mixed workflow / tool versions. Jul 1
Add text that conditionals are optional. Jul 1
Tests for escaping in scripts. Also note that only enum and record types can be typedef-ed Jul 1

Improve lsf batchsystem stability Jul 8
Fix failed job accounting. Jul 6

Add ivar trim command Jul 7

Wunused-but-set-variable is a problem until GCC 6.4 (#277) Jul 1

Created an issue in simd-everywhere/simde that received 5 comments

sse2.h:4872:5: error: 'diagnose_if' attribute expression never produces a constant expression

From PacificBiosciences/pbcopper#11 (comment) where that PR is using SIMDe v0.5.0 clang 11.0.0 "Apple clang version 11.0.0 (clang-1100.0.33.17)") .…

5 comments

"data link" is frequently used but not defined Jul 7
formatting typo in Workflow changelist Jul 7
Include text or link to v1.1 changelist Jul 7

scikit-bio + simde v0.5.0: different numerical output Jul 8

The repository 'https://repo.eduvpn.org/debian stretch Release' no longer has a Release file Jul 7

Should we archive this repository? Jul 3

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