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openpipelines-bio / openpipeline

https://openpipelines.bio
MIT License
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Demultiplication workflow #51

Closed tverbeiren closed 1 year ago

tverbeiren commented 1 year ago

This workflow contains 3 demultiplexers: mkfastq, bcl2fastq and bcl-convert. A fastqc report is generated automatically.

rcannood commented 1 year ago

The ingestion/cellranger_demux can be removed and replaced by demultiplication, no?

@tverbeiren Is this PR ready for merge?

tverbeiren commented 1 year ago

Yes, ingestion/cellranger_demux can be removed.

tverbeiren commented 1 year ago

As far as I'm concerned this PR can be merged.

rcannood commented 1 year ago

@tverbeiren I notice workflows/demultiplication/config.vsh.yaml contains:

functionality:
  name: demux
  namespace: demultiplication

Shouldn't this be called demultiplex instead of demultiplication? Also, the name and namespace is not consistent with the path of the config file.

Proposal: Contents of workflows/demultiplex/demultiplex/config.vsh.yaml:

functionality:
  name: demultiplex
  namespace: demultiplex
# ...

Edit: solved! Renamed to workflows/ingestion/demux.

rcannood commented 1 year ago

Integration test is not working on CI but it does work locally