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bsmn / bsmn-pipeline

BSMN common data processing pipeline
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test first step of containerized, cwl pipeline #20

Closed kdaily closed 5 years ago

kdaily commented 5 years ago

I implemented the first step of the mapping pipeline using bwa mem. It is viewable here:

https://dockstore.org/my-tools/registry.hub.docker.com/dailyk/dockstore-tool-bwa-mem/bwa-mem

This contains a Dockerfile and CWL tool description.

I need to provide a CWL workflow to run this step.

attilagk commented 5 years ago

@kdaily sorry I have just looked at your implementation of mapping. Is it something that could become part of the bsmn-pipeline? I am not familiar with docker; some software needs to be installed before the tool can be used, right?

kdaily commented 5 years ago

Hi @attilagk sorry for not responding here. That's the intention!

I have implemented this entire step now: https://github.com/bsmn/bsmn-pipeline/blob/master/genome_mapping/job_scripts/aln_1.align_sort.sh

The CWL + docker implementation is here: https://github.com/bsmn/bsmn-common-workflow

I'm going to track work over there and close CWL testing related things here. I'll still open tickets re: clarification of the existing pipeline as I continue to implement it there.