Description
Description of the bug
Title: Error running cellrangerarc workflow with 10x Multiome data
Description
I'm encountering persistent errors when trying to run the nf-core/scrnaseq pipeline with 10x Genomics Multiome (RNA + ATAC) data using the cellrangerarc aligner option.
Expected Behavior
According to the nf-core/scrnaseq documentation, the pipeline should support 10x Multiome data analysis with cellrangerarc when providing a CSV with the proper format including the fastq_barcode column.
Actual Behavior
The pipeline consistently fails with the error "Path value cannot be null" in the FASTQC step, despite using the exact format specified in the documentation. The pipeline also shows a warning about the fastq_barcode header being unidentified:
WARN: Found the following unidentified headers in /path/to/sample_sheet.csv:
- fastq_barcode
Additional Information
I've verified all file paths exist and are readable. The issue appears to be with how the pipeline handles the fastq_barcode column, despite it being documented as required for cellrangerarc workflows.
Command used and terminal output
## Steps to Reproduce
1. Prepared a CSV file with the following columns (as specified in documentation):
`sample,fastq_1,fastq_2,fastq_barcode,sample_type`
2. Included both ATAC (with fastq_barcode populated with I2 files) and GEX data (with empty fastq_barcode field)
3. Ran the pipeline with:
nextflow run nf-core/scrnaseq -r 4.0.0
-profile apptainer
--input /path/to/sample_sheet.csv
--fasta /path/to/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/fasta/genome.fa
--gtf /path/to/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/genes/genes.gtf
--aligner cellrangerarc
--save_align_intermeds true
4. Even tried with `--schema_ignore_params fastq_barcode` but still encountered the same error
## Environment
- nextflow version: 24.10.5
- nf-core/scrnaseq version: 4.0.0
- Containerization: Apptainer/Singularity
- Operating system: Linux
## Sample Input File (first few lines)
sample,fastq_1,fastq_2,fastq_barcode,sample_type
LB_brain25_9428_1_HPC,/path/to/LB_brain25_9428_1_HPC_MultiOmeATAC_R1_001.fastq.gz,/path/to/LB_brain25_9428_1_HPC_MultiOmeATAC_R2_001.fastq.gz,/path/to/LB_brain25_9428_1_HPC_MultiOmeATAC_I2_001.fastq.gz,atac
LB_brain25_9428_1_HPC,/path/to/LB_brain25_9428_1_HPC_MultiOmeGEX_R1_001.fastq.gz,/path/to/LB_brain25_9428_1_HPC_MultiOmeGEX_R2_001.fastq.gz,,gex
## Error Message
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK (23)'
Caused by:
Path value cannot be null
Container:
/path/to/singularity/quay.io-biocontainers-fastqc-0.12.1--hdfd78af_0.imgRelevant files
No response
System information
No response