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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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`--cellranger_index` only appears to work if `--validate_params false` provided #340

Open nick-youngblut opened 6 days ago

nick-youngblut commented 6 days ago

Description of the bug

The CellRanger index is a directory of files, and not just one. So, one should provide a directory via --cellranger_index; however, this throws the following error:

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --cellranger_index: '/large_experiments/multiomics/references/cellranger/refdata-gex-GRCh38-2024-A/' is not a file, but a directory (/large_experiments/multiomics/references/cellranger/refdata-gex-GRCh38-2024-A/)

It appears that the parameter validation is checking that the --cellranger_index is a file and not a directory. If I skip the validation via --validate_params false, then the pipeline will complete the CellRanger Count step.

Command used and terminal output

nextflow run main.nf \
   -profile test_full,singularity \
   -process.executor slurm \
   -process.queue cpu_batch \
   --aligner cellranger \
   --cellranger_index /large_experiments/multiomics/references/cellranger/refdata-gex-GRCh38-2024-A/ \
   --outdir test_run_output \
   --validate_params false

Relevant files

No response

System information

Nextflow version: 23.10.1.5891 Hardware: HPC Executor: SLURM Container engine: Apptainer OS: Ubuntu Version of nf-core/scrnaseq: 2.6.0