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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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No matrix file in STAR outputs #134

Closed Vivian-chen16 closed 1 year ago

Vivian-chen16 commented 2 years ago

Description of the bug

Hello,

I've successfully finished running scrnaeq with --aligner star on single AWS instance but couldn't find the count results (i.e. barcode.tsv, features.tsv and matrix.mtx) in the out directory. The output structure I had is identical as this: https://nf-co.re/scrnaseq/results#scrnaseq/results-27f37ab827b3f72e8e305256a9c59a37bb85ef83/aligner_star/star/ Is there any other options I should include to generate them?

Any suggestions are appreciated!

Command used and terminal output

$ nextflow run nf-core/scrnaseq --input sample21476_CTX-sheet.csv --outdir sample21476_CTX --genome_fasta ./refdata-gex-GRCh38-2020-A/fasta/genome.fa --gtf ./refdata-gex-GRCh38-2020-A/genes/genes.gtf --protocol 10XV2 --aligner star -profile docker -bg

Relevant files

Screen Shot

System information

No response

Vivian-chen16 commented 2 years ago

For those who also wonder about this - the rest of STAR outputs are actually under work directory rather than outdir.

grst commented 2 years ago

If they are not getting published to the results directory, that's a bug (which should be easy to fix)!

One should never have to look into the work dir to obtain results.

Vivian-chen16 commented 1 year ago

fixed in added an option to convert star count matrix !