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Michael R. Crusoe mr-c

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Common Workflow Language co-founder & CWL Project Lead. Debian Developer volunteer for the Debian-Med (bioinformatics) team. #SciWorflows #FreeOpenStandards

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Pinned

common-workflow-language/common-workflow-language Public

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

Common Workflow Language 1.3k 188
common-workflow-language/cwltool Public

Common Workflow Language reference implementation

Python 268 186
common-workflow-language/schema_salad Public

Semantic Annotations for Linked Avro Data

Python 58 50
shouldacite Public

Should you cite this software?

CSS 25 2
common-workflow-language/cwlprov Public

Profile for provenance research object of a CWL workflow run

12 2

1,777 contributions in the last year

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Activity overview

Contributed to common-workflow-language/cwltool, DataBiosphere/toil, common-workflow-language/schema_salad and 5 other repositories

Contribution activity

January 2022

Created 40 commits in 11 repositories

Created 2 repositories

mr-c/cereal C++ Jan 17
mr-c/mypy_primer Python Jan 6

Created a pull request in DataBiosphere/toil that received 6 comments

ask cwltool to cleanup, if installed

Changelog Entry To be copied to the draft changelog by merger: CWL: at the end of a job, ask cwltool to cleanup Reviewer Checklist Make sure it…

+11 −0 • 6 comments

Opened 22 other pull requests in 7 repositories

common-workflow-language/cwltool 6 merged 1 open

test_bad_stdout_expr_error needs docker Jan 19
adjustment for docker build Jan 17
Drop Python 3.6 Jan 16
expand stdin shortcut even when an ID is preset Jan 16
DO NOT MERGE: proof of concept: update v1.2 schema for pure strings enum symbols Jan 15
GA: simplify pip caching Jan 10
remove an Any type hint Jan 6

common-workflow-language/schema_salad 5 merged

Fix mergify config Jan 17
Java Codgen: use List<String> when applicable Jan 14
typescript: add documentation generation command Jan 6
java: pom.xml bump some versions Jan 6
javacodegen scope check: chop off the correct end of the fragment Jan 5

common-workflow-lab/wdl-cwl-translator 4 merged

Use cache results to speed up cwltest{,_big} Jan 18
include checksums in functional test defs Jan 10
add missing file for the big CWL functional tests Jan 10
bcftools_stats: colocate optional fastaRef & index Jan 10

USCiLab/cereal 2 open

common-workflow-lab/cwljava 1 open 1 merged

Enum symbols are plain strings Jan 14
scope check: chop off the correct end of the fragment Jan 5

common-workflow-language/cwl-v1.2 1 open

enum symbols are plain strings Jan 14

hauntsaninja/mypy_primer 1 merged

Include python-sop Jan 6

Reviewed 32 pull requests in 11 repositories

common-workflow-lab/wdl-cwl-translator 10 pull requests

delete and replace old files. Also delete references to oop Jan 19
fix indentation in command string Jan 19
Use a convert function like the former main file Jan 19
complete the adoptation of main.py Jan 19
Small improvements Jan 18
handle all validateOptimus files Jan 13
Adopting the validateOptimus files Jan 13
translate bcftools_annotate Jan 11
start bcftools_stats.wdl adoptation with main_oop Jan 10
Bcftools annotate Jan 6

carpentries-incubator/cwl-novice-tutorial 8 pull requests

Fix indentation of first example Jan 18
Add YAML prerequisite and link to YAML guide Jan 18
Add keypoints Jan 18
Fix typos Jan 18
Update link Jan 8
Align comments Jan 8
Setup git repo Jan 8
Provide missing URLs Jan 7

common-workflow-language/cwltool 5 pull requests

docker: enforce cores ResourceRequirement if requested Jan 17
GA: simplify pip caching Jan 13
Protect ruamel from blank comment strings when making templates Jan 6
Update how to setup pip environment Jan 6
Initial support CUDARequirement extension Jan 3

DataBiosphere/toil 2 pull requests

common-workflow-language/cwl-v1.2 1 pull request

enum symbols are plain strings Jan 19

conda-forge/cwltool-feedstock 1 pull request

[bot-automerge] cwltool v3.1.20220117131913 Jan 17

biocompute-objects/BCO_Specification 1 pull request

22.01 Jan 15

common-workflow-lab/cwljava 1 pull request

Enum symbols are plain strings Jan 14

conda-forge/schema-salad-feedstock 1 pull request

Rebuild for python310 Jan 14

rabix/sbpack 1 pull request

change the ID delimiter from : to @ Jan 12

common-workflow-language/schema_salad 1 pull request

Fix initialization of class fields with instance type "string" Jan 3

Created an issue in common-workflow-language/schema_salad that received 8 comments

metaschema predicates pollute salad document namespace

Alternative title: CWL enum symbols get fully expanded instead of being left as pure strings Source issue: common-workflow-lab/cwljava#70 For examp…

8 comments

Opened 8 other issues in 6 repositories

common-workflow-lab/wdl-cwl-translator 3 open

common-workflow-language/schema_salad 1 open

schema-salad-tool --print-doc / schema-salad-doc: privacy leak Jan 19

lepture/mistune 1 open

2.0.x regression in multi-line list entry handling Jan 17

mypyc/mypyc 1 open

mypyc 0.910 - 0.931 test failures on i686 (and armel, armhf) Jan 10

common-workflow-language/cwltool 1 open

CWLProv: add option exclude raw copies of the data Jan 6

DataBiosphere/toil 1 open

CWL: Implement the new cwltool:CUDARequirement resource requirement Jan 5