GATK4 is DFSG compatible, GATK3 still has a non-DFSG core https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl is entirely based upon free software, but the reference libraries are quite large
2017-08-11 18:57 GMT+03:00 Steffen Möller <[email protected]>: > Hello, > > I had an exchange with Stian yesterday about what CWL workflow of his > database he would propose to use as an experience-gathering example. He > proposed the GATK workflow by Farah Zaib Khan et al. for being good to > cite about workflows and reproducibility. > > https://doi.org/10.1186/s12859-017-1747-0 > https://github.com/skanwal/GATK-CaseStudy/tree/master/CWL > > We have BWA, GATK and Picard Toolkit already in Debian from what I > understand (not sure about the state of GATK). Stian had pointed to > https://github.com/h3abionet/h3agatk/blob/master/workflows/ > GATK/GATK-complete-WES-Workflow-h3abionet.cwl > as a current variant of the same, but then again, I would not mind to > start with a smaller one. Any comments? > > The main point for me is to have a small test case for running this > workflow repeatedly. We would hence also need to decide on appropriate > test data at some point. Should we also introduce a package like > "genome-human"? > > Best, > > Steffen > > > -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project <http://www.commonwl.org/> https://impactstory.org/u/0000-0002-2961-9670 [email protected] +1 480 627 9108
