Hi I am trying to use scrnaseq pipeline for GEX+TCR analysis nf-core #scrnaseq

Hi! I am trying to use scrnaseq pipeline for GEX+T...

Marcel Costa-Garcia

07/23/2026, 2:09 PM

Hi! I am trying to use scrnaseq pipeline for GEX+TCR analysis with cellranger multi pipeline. I am struggling with the VDJ reference parameters. This is my launcher command:

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NXF_VER=25.10.4 nextflow run nf-core/scrnaseq \
    --input samplesheet.csv \
    --outdir ../PROCESSING \
    -profile apptainer \
    --aligner cellrangermulti \
    --igenomes_base ~/Shared-MarcelCosta/references/cellranger-10.0.0 \
    --fasta ~/Shared-MarcelCosta/references/cellranger-10.0.0/genome.fa \
    --gtf ~/Shared-MarcelCosta/references/cellranger-10.0.0/genes.gtf \
    --cellranger_vdj_index ~/Shared-MarcelCosta/references/cellranger-10.0.0/regions.fa

And the pipeline tries to find the reference in the work directory in:

references/vdj/regions.fa/fasta/regions.fa

However, when I go to the work directory the reference is in:

references/vdj/regions.fa

Any clue if I should specify the reference in a different way? Thanks!!

Marcel Costa-Garcia

07/27/2026, 8:53 AM

Ok, I think I have found how to properly execute the command. VDJ reference must point to the parental directory as it is provided by 10X (the pipeline expects so).

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NXF_VER=25.10.4 nextflow run nf-core/scrnaseq \
    --input samplesheet.csv \
    --outdir ../PROCESSING \
    -profile apptainer \
    --aligner cellrangermulti \
    --igenomes_base ~/Shared-MarcelCosta/references/cellranger-10.0.0 \
    --fasta ~/Shared-MarcelCosta/references/cellranger-10.0.0/genome.fa \
    --gtf ~/Shared-MarcelCosta/references/cellranger-10.0.0/genes.gtf \
	--cellranger_vdj_index ~/Shared-MarcelCosta/apps/cellranger-10.0.0/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0/

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