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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Include --expect-cells when using --aligner cellranger #182

Open adairama opened 2 years ago

adairama commented 2 years ago

Description of feature

As discussed in the Slack Channel for scrna-seq on 23rd September 2022:

It will be good to allow --expect-cells in the run with --aligner cellranger option for scrnaseq pipeline. Since the expected cells can vary between samples (e.g. 6000 for sample 1, 3000 for sample 2), it will be good have this as a column in the sample metadata.

Gregor Sturm suggested related issue: https://github.com/nf-core/scrnaseq/pull/90#issuecomment-1132799761

apeltzer commented 2 years ago

CellRanger v.7 (which is included inthe pipeline) should auto-detect this btw, so actually not really needed. Not sure if its more accurate if we specify it (and what happens if we specify a wrong value here?).

grst commented 1 year ago

also universc should consume the expected_cells column. I suggest to add a value auto as default for cellranger.

grst commented 3 weeks ago

Even if it might not be necessary for cellranger, this flag should behave correctly and pass the value if it's specified to all aligners that support it. The default should be auto.

Universc shall be removed, see #289