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hi @njspix looks like this might be a nice addition to the pipeline. the branches might have diverged a bit so, might need some care there. How much work do you anticipate is left to push this through ? and if I can be of any help... |
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Hey @sateeshperi thanks so much for checking in! I would love to get this pushed through as well. However, as I am working on it, I've done quite a bit of reworking, maybe even enough for a major version bump. Things that make sense for two aligners (one set of options for one, another set for the second) start to make less sense for 3 aligners, and there are a lot of common options (e.g. how much coverage to require for a methylation call, whether to do directional alignment, and if so, how, etc) that with some finagling can be generalized to all 3 aligners. Thus, you'll see significant changes to the config and parameters. I think most things are pretty close to working, but unfortunately other responsibilities have taken priority the last few months. I would estimate it would take me about a weeks' worth of solid effort to put this in a state where I was ready to sign off on every aspect of the workflow, much of that would be testing with various combinations of parameters. If you would like to take a look through the schema and let me know what you think of the changes I made, that would be most welcome! Module updates etc would be welcome as well... I hope to get back to working on this part-time in a few weeks, please let me know your thoughts! |
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I agree this would be a major version bump on its own and I understand the consolidation of params that this re-work involves and thank you for thinking through it. just want to thrown in there is an issue to add in another aligner too - bismark-minimap2 #257. |
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Awesome, thank you so much! Yes, I wouldn't mind adding in support for minimap2 as well - better to do it all at once! :) |
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Hello all,
I've put together a draft PR incorporating the Biscuit suite of tools. This is still a work in progress, but I wanted to open the PR and get your feedback.
I did make a few changes to the rest of the workflow. These include version bumps, as well as re-naming and re-organizing a couple of the parameters. I moved a couple of parameters from the 'Bismark options' section to the 'alignment options' section, as these parameters (e.g. 'directional') apply to more than one aligner. I also expanded the 'methylation calling options' section (or created it? I can't remember), which again contains general options (e.g. minimum coverage depth) that apply to multiple tools.
Todos include updating docs (usage, output, changelog, readme), adding CI tests/test profile for the Biscuit workflow, and running various combinations of input and parameters...
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Thanks much!