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When aligner is cellrangerarc the step MTX_TO_SEURAT failed #299

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wzheng0520 opened this issue Jan 31, 2024 · 3 comments
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When aligner is cellrangerarc the step MTX_TO_SEURAT failed #299

wzheng0520 opened this issue Jan 31, 2024 · 3 comments
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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.

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@wzheng0520 wzheng0520 added the bug Something isn't working label Jan 31, 2024
@heylf heylf self-assigned this Feb 2, 2024
@heylf heylf mentioned this issue Feb 2, 2024
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heylf commented Feb 2, 2024

Should be fixed with this PR

@grst grst mentioned this issue Mar 5, 2024
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grst commented Mar 13, 2024

Fixed in dev

@grst grst closed this as completed Mar 13, 2024
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grst commented May 8, 2024

Apparently still an issue in 2.6.0. We need #290

@grst grst reopened this May 8, 2024
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299-when-aligner-is-cellrangerarc-the-step-mtx_to_seurat-failed nf-core/scrnaseq
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