Michael Kotliar

ResourceRequirement of CWL file is ignored when CommandLineTool is run from the Workflow.

1

When submitting the following CWL `CommandLineTool` on LSF with Toil 5.5.0 I can see that the node has been requested with the proper memory and cpu parameters. ```yaml cwlVersion: v1.0...

Tool fails with "path is outside the designated output directory" if input has secondaryFiles and using InitialWorkDirRequirement

5

## Expected Behavior When staging input file to the output directory the secondaryFiles should be also staged into the same directory, otherwise tools fails to execute with "path is outside...

Not yet tested. Airflow 2.2.0 cwltool 3.1.20211004060744

**Is your feature request related to a problem? Please describe.** When packing the workflow with `cwltool --pack` command, it cannot be parsed into CWLDAG **Describe the solution you'd like** Make...

**Describe the bug** If CommandLineTool has `id` field then all inputs and outputs get prepended by this id. This results in failure while contructing CWLDAG **To Reproduce** Run [cwl-v1.1](https://github.com/common-workflow-language/cwl-v1.1/tree/be5ee84de20d41b6d7d94b3d2a71ddd591d1bf73) conformance...

Configure Jenkins to run conformance tests properly

- cellranger * cellranger-aggr.cwl * cellranger-arc-aggr.cwl * cellranger-arc-count.cwl * cellranger-arc-mkref.cwl * cellranger-count.cwl * cellranger-mkref.cwl * cellranger-reanalyze.cwl - gat * gat-run.cwl - gffread * gffread.cwl - gsea * gseapy.cwl - haltools...

The structure of the repository

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Here we need to decide the structure of the this repository. As it was agreed, every tool should be placed in a separate directory. The questions are: - should we...

fastq_dump.cwl might have some problems when running without Internet connection

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It looks like [fastq_dump.cwl](https://github.com/common-workflow-library/bio-cwl-tools/blob/release/sratoolkit/fastq_dump.cwl) might have some problems when running without Internet connection. fastq-dump downloads something even when extracting data from the previously downloaded sra file.

Split view by dataset

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Hello! Is there any functionality in the browser that would allow to split the view by dataset or, let's say, by time point? We have data aggregated from 4 time...