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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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Bootstrap plots checkpoint to report directory #21

Closed dlaehnemann closed 4 years ago

dlaehnemann commented 4 years ago

This PR also harmonizes the naming of the rst-files for plots used in the HTML report.

Also, it seems like the wildcards used in the new directory(patterns=) keyword are not available upon parsing of the rst file (as is suggested in the snakemake docs, at least the snakemake.wildcards.transcript from the rule plot_bootstrap simply does not appear in the caption in the produced report.

dlaehnemann commented 4 years ago

@johanneskoester This requires the GitHub Actions Docker to be updated to snakemake 5.13.0 via this PR (plus then a new release of GitHub Actions): https://github.com/snakemake/snakemake-github-action/pull/5

johanneskoester commented 4 years ago

Done!

dlaehnemann commented 4 years ago

@johanneskoester Then feel free to review and merge... ;)

dlaehnemann commented 4 years ago

Just realised one more question: Should we attempt the same with the fgsea checkpoint? It should also work and would simply produce several plots in one run of the rule instead of only one plot per run of the rule...

johanneskoester commented 4 years ago

This PR also harmonizes the naming of the rst-files for plots used in the HTML report.

Also, it seems like the wildcards used in the new directory(patterns=) keyword are not available upon parsing of the rst file (as is suggested in the snakemake docs, at least the snakemake.wildcards.transcript from the rule plot_bootstrap simply does not appear in the caption in the produced report.

This should work now with snakemake 5.14.

johanneskoester commented 4 years ago

Given that it works now, do you want to change the caption text to make use of it?

dlaehnemann commented 4 years ago

Oh, the captions were using it anyways -- it didn't throw an error and just kept them blank, so I left that in awaiting the fix. But I now touched up the captions a bit more, adding in the respective wildcard for the fgsea gene set plots and putting separate sentences on separate lines.