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Adding cellrangermulti subworkflow #276
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Ok. I think I'm done with the documentation. |
I don't think lint will pass before the template update is merged. However, since this is such massive PR, I'd do that after this one gets merged to dev to avoid further disruptions. |
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Are we there then? I don't think there's anything pending for now.
Hi @grst, I think so. The last things were the documentation and the things you had brought. This was the comment summarising it: #276 (comment) We can have a last look on that, and open follow-ups, otherwise, it is. |
I have added a follow-up ticket for the open points: #332 |
Close #247
Close #313
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).Context
Hi guys,
Although not finished yet because it would still required updating the parameters schema, defaults and documentation, I am already opening the PR so we can all take a look at it and discuss any modifications required before merging and also, give it a round of tests and define how we want some parameters to be.
I used the templates provided by @klkeys
Usage context
![image](https://private-user-images.githubusercontent.com/7727714/285190770-249cd849-f626-4d7a-9e0c-fb4a8aef743f.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.MDl1QQJoeOyFQ-Un3jvDQuruENrxuaJ3T_V3OuZueEs)
samplesheet
To use it, samplesheet requires an additional parameter so that we can properly mix the different feature types given per sample.
Supporting files
Right now, all the supporting files have been added as parameters, for example,
cmo_barcode_csv
,beam_antigen_csv
, etc. .... which means they will work in a dataset manner, being the same for everything given in the samplesheet, instead of samplesheet base if they were added as columns in the samplesheet.My main question here is, what should it be the desired approach?
Other stuff
Of course there might still have things to clear or finish that I might have overlooked since there is quite a lot on it, so, I request your help on spotting it.