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inab / Wetlab2Variations

Wetlab2Variations Workflow Demonstrator
Apache License 2.0
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CWL step connection #8

Open rtonda opened 5 years ago

rtonda commented 5 years ago

Use variables to connect steps to avoid explicit declaration of inputs and outputs. I.e:

Step1 input: My_fastq_1.fastq.gz Step1.output: $(basename step1.input).trimmed.fastq.gz Step2 Input: $(step1.output) Step2 Output: $(basename step2.input).bam

jarnolaitinen commented 5 years ago

I am not sure if I got it right. There is an input file (it will be in given by the user in a yml or otherwise) such as the My_fastq1.gz and you want to run the CWL jobs with that? I think the CWL workflow will do it with the variables with defined type. See:
https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/examples/1st-workflow.cwl which calls https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/examples/tar-param.cwl