search

nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
178 stars 154 forks source link

When aligner is cellrangerarc the step MTX_TO_SEURAT failed #299

Open wzheng0520 opened 4 months ago

wzheng0520 commented 4 months ago

Description of the bug

When we choose cellranger arc as aligner, the step MTX_TO_SEURAT failed and generate the following error message:

Attaching SeuratObject
Error: Cannot find expression matrix at matrix.mtx.gz
In addition: Warning message:
In normalizePath(path = all.files[[i]], winslash = "/") :
  path[1]="matrix.mtx.gz": No such file or directory
Execution halted

I think it might cause by when we choose the cellrangerarc, the whole filtered_feature_bc_matrix folder is copied into the workdir, however based on how cellranger works, the pipeline should copy the files inside filtered_feature_bc_matrix.

Command used and terminal output

No response

Relevant files

No response

System information

No response

heylf commented 4 months ago

Should be fixed with this PR

grst commented 3 months ago

Fixed in dev

grst commented 1 month ago

Apparently still an issue in 2.6.0. We need #290