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sickle-in-africa / sequence-analysis-pipelines

a library of sequence analysis pipelines for human genomic medicine
GNU General Public License v3.0
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re-writing the library in another language? #10

Open jackmo375 opened 4 years ago

jackmo375 commented 4 years ago

We are probably reaching the limits of bash and the library will get harder and harder to maintain as it grows. Should we consider re-writing in python, perl, wdl, something else? To resolve this issue we should decide:

  1. should the pipelines be re-written in a more feature-rich language?
  2. should we use more than one language?
  3. which language(s) should we chose?
jackmo375 commented 4 years ago

Maybe we should consider a workflow domain specific language (DSL) to write the pipelines in. Something like openWDL might be good, it was developed by the broad institute for genome sequence analysis and I know malariaGEN uses it...

I am seeing that H3Bionet has already produced some workflows in the following workflow description languages:

  1. CWL
  2. Nextflow

I am seeing that Nextflow is available on CHPC. CWL is (I think) integrated with the Galaxy platform which is a plus.