Using local reference instead of connecting to iGenome

Ask for help
,
1

Hi!

I am trying to run “scRNAseq” nf-core pipeline with that command:

NXF_VER=25.10.4 nextflow run nf-core/scrnaseq \
    -profile test \
    --aligner cellranger \
    --fasta ~/Shared-MarcelCosta/apps/cellranger-10.0.0/refdata-gex-GRCh38-2024-A/fasta/genome.fa \
    --cellranger_index ~/Shared-MarcelCosta/apps/cellranger-10.0.0/refdata-gex-GRCh38-2024-A/fasta/genome.fa.fai \
    --gtf ~/Shared-MarcelCosta/apps/cellranger-10.0.0/refdata-gex-GRCh38-2024-A/genes/genes.gtf.gz \
    --outdir PROCESSING

However, I get this error:

* --igenomes_base (s3://ngi-igenomes/igenomes/): could not validate file format of 's3://ngi-igenomes/igenomes/': Access Denied (Service: S3, Status Code: 403, Request ID: 4F61R9KM8W39WSMT, Extended Request ID: qa4D4BHgJMfa2KLuSmPYARTuZnKR/ObNHgeSSM6ur226/3vZVhr/BYGvg77an3ssxHERDxzWFZ20SBSWl1oofjWAUIeRrTvz) (SDK Attempt Count: 1)

I don’t want to use igenomes because I have already download the reference genomes. Is there a way to specify not to fetch it? I am missing any parameter?

Thanks!

2

Adding this parameters doesn’t avoid the error:

--genome null --igenomes_ignore
3

At the end, what worked for me (thanks to @pontus ) was:

NXF_VER=25.10.4 nextflow run nf-core/scrnaseq \
    --input samplesheet.csv \
    --outdir ../PROCESSING \
    -profile apptainer \
	--aligner cellranger \
    --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