refactor of pipeline #52
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All relevant information from that branch now appears to be merged. These are the single-cell progeny production pilots.
This is more Illumina 10x sequencing of some of the transcriptomes. Also fixed mis-specification of hashing trial 3 without NH4Cl
merge David's updates into new refactored pipeline branch
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@jbloom That sounds like a good strategy. We can add back the analysis notebooks one at a time and review them. I am going to make sure this runs on my local directory before I approve the pull request. I've been getting an error that I think is related to the new snakemake/jupyter integration. I will try this new version and see if it resolves the issue. |
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This looks good. The jupyter-nbconvert issue was fixed by changing the permissions. The pipeline runs without error and the output that I spot checked looks good. |
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@dbacsik, this is my pull request that refactors the pipeline. If this looks good to you, we can merge it into
mainand then work from there. Lots of changes! Main ones:config.yamlas you are familiar with.snakemakecapability for this (see use newSnakemakeJupyter notebook integration #46).report.htmlfile is now written toresultsand isn't tracked for now as it gets too many differences.Note that this does not have the analysis notebooks, so we need to add those. But I thought we could try to get this on
mainand then make future pull requests to it to consolidate the other branches back in. Does that sound good?