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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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cellrangerarc test failing - null path? #374

Open davhum opened 1 month ago

davhum commented 1 month ago

Description of the bug

I am having trouble getting the following test to work. Any clues to what I am doing wrong.

The command I ran was:

nextflow run nf-core/scrnaseq -profile test,docker --outdir /mnt/bdsf/test_arc --aligner cellrangerarc

Output error (do you need more info?)

Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (2)'

Caused by: Path value cannot be null

Workflow: nf-core/scrnaseq: v2.7.1-g4171377 Nextflow: 24.04.4

Command used and terminal output

No response

Relevant files

No response

System information

No response

j-andrews7 commented 1 month ago

Also hitting this with the same versions and real data.

grst commented 1 month ago

Cellrangerarc is currently not properly tested, see #290.