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I converted a working draft-3 CWL file to a version 1.0 CWL file by changing the following.
1. `"cwlVersion": "draft-3",` -> `"cwlVersion": "v1.0",`
2. `"inputs"` -> `"in"` for all STEP inputs (but…
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Essential:
* Author
* Description
Others:
* Topic (keywords?)
* License of wrapped tool (#4)
See https://github.com/Barski-lab/workflows/blob/master/tools/bamtools-stats.cwl for ideas
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It'll allow integrating valuable descriptions such as https://github.com/common-workflow-language/workflows/blob/master/tools/GATK-PrintReads.cwl with Bio.Tools & co
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Command used:
```
./cwlexec /home/johnsoni/Innovation-Pipeline/workflows/QC/qc_workflow_wo_waltz.cwl ~/Innovation-Pipeline/test/workflows/EZ_QC_test.yaml
Error: Could not find or load main class …
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Currently the validation script is down to 30 issues, the logs can be found [here](https://docs.google.com/document/d/18p2O4jboozcZXDsXDh8glom9DoE6FYAyxfNd5OQcI64/edit?usp=sharing).
The remaining iss…
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Discussion and original issue is here: https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/2
Short summary:
If I use as input to a step and I put a directory array (Directory[]) …
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Hi,
Thanks for the methylation analysis pipeline.
I was testing a human WGBS data with msPIPE, and I used UCSC hg38 for reference. When running with run_MethylSeekR.pl, I got the following error…
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### Description
The turtle file with RDF(S) of the CWL SALAD Schema retrievable under [http://commonwl.org/v1.2/cwl.ttl](http://commonwl.org/v1.2/cwl.ttl) (or alternatively by running `schema-salad-t…
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**Describe the bug**
After upgrading to v1.8.1, VPC flow logs are sent to newly named CloudWatch log groups. This breaks the dynamic log partitioning feature of LZA.
**To Reproduce**
1. Make …
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Is a `ResourceRequirement` in the `hints` section intended as a best-effort to provision the specified amount of resources? If the answer is no, that hints, if they are supported by the runner, are st…