A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi, I’m trying to run the pipeline with aligner=cellrangermulti and encountered the following error :
```[error] Pipestance failed. Error log at:
  QVIXC018A1/SC_MULTI_CS/PARSE_MULTI_CONFIG/fork0/chnk0-u004ddb9dd0/_errors
  
  Log message:
  [gene-expression] section with a path to the transcriptome reference is a required input (even if only antibody-data is present).
  
  Waiting 6 seconds for UI to do final refresh.
  Pipestance failed. Use --noexit option to keep UI running after failure.```

I found a mention of this error here: <https://nfcore.slack.com/archives/CHN5BV5DW/p1735933570004519?thread_ts=1733332324.963749&amp;cid=CHN5BV5DW> Howeve I’m already using full hard link paths for all my parameters.

Here’s the parameters i used:
```nextflow run nf-core/scrnaseq -r 4.0.0 -profile cfc \
--input 'sample_sheet_cellranger_2.csv' \
--outdir 'out_scrnaseq_cellranger_1' \
--aligner 'cellrangermulti' \
--protocol 'auto' \
--skip_cellrangermulti_vdjref \
--fb_reference 'feature_barcode_sheet_2.csv' \
--igenomes-ignore \
--fasta 'test_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz' \
--gtf 'test_gtf/homo_sapiens/Homo_sapiens.GRCh38.113.gtf.gz' \```