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Hello, I wanted to know if there was a way to specify the cellranger version used. For single cell analyses, using different versions of cellranger can affect the data, and for projects with multiple …
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### Description of feature
[cellranger_count.py](https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/cellranger/count/templates/cellranger_count.py) currently just uses `subprocess.run` f…
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While loading the cellranger data (10X), this is the error I encounter.
-- [4/14] Parsing "/jsimonlab/users/bshim/Shuntaro_scRNA_TCR/Pool142_Cellranger/Pool142_Pt1_R/outs/all_contig.bam.bai" -- …
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I'm following the "[read the docks](https://cumulus.readthedocs.io/en/stable/cellranger/fixed_rna_profiling.html)" input protocol for the CSV file and other Terra inputs and am receiving an error rela…
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### Description of the bug
Hey all, I am looking at the `cellranger mkref` module and noticed that automatic available resources detection has been added, but I think I have spotted an inconsistenc…
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Hi! I ran into this error:
“Error in checkGrep(grep(".A.txt", files)) :
Improper folder specification; file missing / extra file present. See documentation
Calls: importMito -> checkGrep
E…
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**Snakemake version**
snakemake version 8.12.0
**Describe the bug**
I can run my snakemakefile interactively without any issue ```salloc --nodes=1 --partition=acompile --ntasks=1 --time=01:00:…
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This txt file link is already 404: Not Found.
wget -qO- https://raw.githubusercontent.com/10XGenomics/cellranger/master/lib/python/cellranger/barcodes/3M-february-2018.txt.gz | gunzip - > 3M-februa…
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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue for this…
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- [ ] scRNA-seq
- https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#runmkref
- [ ] What about scATAC-seq