Hello! I have been trying to use scrnaseq to map CITE-Seq samples for several days now and I have been entirely unsucessful. The pipe always breaks on the antibody file mapping phase. At first I thought the issue might be with cellranger count and tried using cellranger multi but both should work and I even managed to map the samples with just using cellranger count. This all works as long as you provide the program with the info of which type of a file it is, i.e. gene expression or anitbody capture. fastqs sample library_type /data/loc/FASTQ/ sample_1_AB Antibody Capture /data/loc/FASTQ/ sample_1 Gene Expression So, it works with just cellranger, but when I try to get it running with scrnaseq pipe I keep getting the same very long error:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT

Process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (sample_1_FB) terminated with an error exit status (1)

2024-09-05 11:57:34 [runtime] (failed)          ID.<http://sample_1_FB.SC|sample_1_FB.SC>_<http://RNA_COUNTER_CS.SC|RNA_COUNTER_CS.SC>_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY

[error] Pipestance failed. Error log at:

sample_1_FB/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u004ed98050/_errors

I can add way more lines or send the log but I think the issue is that the nfcore's scrnaseq pipe is not transmitting the info about GEX or AB from the sample table to the cellranger properly. And exactly the same error happens regardless if I use multi or count version of cellranger. Or if I specify the chemistry in an argument or protocol column in a sample table. just for clarity here's the command I run:

nextflow run nf-core/scrnaseq -r 2.7.1

-profile cluster

--aligner cellranger

--skip_fastqc true

--input /location/cellranger_sample_sheet.csv

--fasta /location/fasta/genome.fa

--gtf /location/genes/genes.gtf

--fb_reference /location/CITE_seq_barcodes.csv

--outdir /location/01_mapped/

-c /location/nextflow_sc_extraresource.config

-w /location/username/work/

--protocol auto

And the cellranger_sample_sheet.csv looks like this: sample fastq_1 fastq_2 feature_type sample_1 /location/sample_1_S1_L005_R1_001.fastq.gz /location/sample_1_S1_L005_R2_001.fastq.gz gex sample1_FB /location/sample_1_FB_S1_L005_R1_001.fastq.gz /location/sample_1_FB_S1_L005_R2_001.fastq.gz ab So the long story short, I think the main issue is that I don't know how to properly configure scrnaseq pipeline for cite-seq samples.