legacy
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common-workflow-library
Deprecated
I was looking for an example where the CommandLineTool and Workflow are in one file, and in trying to run https://github.com/common-workflow-language/workflows/blob/master/workflows/make-to-cwl/dna.cwl I get: ``` $ cwltool ~/workflows/workflows/make-to-cwl/dna.cwl /home/ubuntu/.virtualenvs/p2_cwl/bin/cwltool 1.0.20160523144113 No...
At least when running samtools-faidx without docker, the input fasta (.fa) file is replaced with a symlink pointing to itself: ``` bash [samuel 002-resequencing]$ ll *fa lrwxrwxrwx 1 samuel samuel...
This change just moves the docker import to the hints section, in the `bwa aln` tool. Note that this will break stuff because of [this bug in cwltool](https://github.com/common-workflow-language/cwltool/issues/80), so it...
Hello @tetron & @portah, Is there "Git-sized" test-data for this workflow? For the sake of maintenance I think we shouldn't include anything in this repo that doesn't have tests +/or...
When trying to run the compile example, the provided command `/cwl-runner --basedir ${PWD} compile1.cwl` does not work (with `cwltool`, at least), even when disregarding the leading slash of the command....
The first encounter with the cwl for executing something needs to be as simple as ... donno ... something really simple. The traditional "Hello world!" for instance does not need...
> CWL is designed to express workflows for data-intensive science, such as Bioinformatics, > _**Medical Imaging**_, Chemistry, Physics, and Astronomy. Can someone point me to any examples of medical imaging...
@mr-c please create a proper class to handle the paired-end reads input to ray assembler invoked via ray.cwl
