andrewjesaitis / cwl-tutorial Goto Github PK
View Code? Open in Web Editor NEWTutorial for the Common Workflow Language using SnpEff
License: MIT License
Tutorial for the Common Workflow Language using SnpEff
License: MIT License
Hi Andrew, first thank you for the tutorial, I had exactly what you had with the, "either too simplistic to be useful or too complex". Excuse any noob GitHub etiquette, long time lurker, first time posting.
I encountered a permissions issue when following the tutorial that is resolved when following the advice under the section of "boot2docker" in the cwltool installation (Ubuntu 18.04 LTS (main OS), Docker version 18.09.2, build 6247962, and cwltool 1.0.20190228155703).
The issue can be resolved by adding flags for the directory prefixes when calling cwltool.
cwltool --tmp-outdir-prefix=/path/to/the/cwltool/tutorials/by/jesaitis --tmpdir-prefix=/path/to/the/cwltool/tutorials/by/jesaitis snpeff-workflow.cwl 1kg-job.yml
Hi, the post https://andrewjesaitis.com/2017/02/common-workflow-language---a-tutorial-on-making-bioinformatics-repeatable/ it refers to a --leave-tmpdirs
argument to cwltool
but the actual flag is --leave-tmpdir
(without the s
).
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