Option to use cellranger pre-built reference

[svigneau]

Description of feature

It would save time and computing resources if the pipeline could take cellranger pre-built references (downloadable here) instead of rebuilding them from FASTA and GTF files when using the cellranger or cellrangermulti aligner parameter.

[grst]

This should be fixed on dev, could you give it a try?

[svigneau]

Thanks for pointing this out!

I tried the following, which worked out fine:

1. Download a pre-built cellranger reference from this page using:

curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz"
tar -xzf refdata-gex-GRCh38-2024-A.tar.gz

2. Modify the conf/igenomes.config file by adding the following genome:

'GRCh38-2024-A' {
     cellranger = '/path/to/refdata-gex-GRCh38-2024-A/'
 }

3. Add the following line to my params.yaml file:

genome: 'GRCh38-2024-A'

4. Run with:

nextflow run /path/to/scrnaseq/main.nf -params-file params.yaml -c nextflow.config

It feels a bit odd having to modify the pre-defined igenomes.config file, though, instead of being able to pass a custom genomes.config file. What do you think about adding this functionality?

[grst]

Hi @svigneau,

the intended way to provide cellranger references would be via the --cellranger_index parameter.
It should also already be possible to override the genomes configuration in a custom config file and specify it with -c. Did you try that?

[svigneau]

Thanks for the follow-up!

I tried both options and both worked :)

Here is what I did for reference:

• Using the cellranger_index parameter:
  • Add cellranger_index: '/path/to/refdata-gex-GRCh38-2024-A/' to theparams.yaml file
  • Run locally with nextflow run /path/to/nf-core/scrnaseq/main.nf -params-file params.yaml -c nextflow.config
• Using a cellranger-genomes.config file:
  • Create a cellranger-genomes.config file containing:

    params {
        genomes {
            'GRCh38-2024-A' {
                cellranger = 'gs://svigneau-b2/references/refdata-gex-GRCh38-2024-A/'
            }
        }
    }
    

  • Add genome: 'GRCh38-2024-A' to the params.yaml file
  • Run locally with nextflow run /path/to/nf-core/scrnaseq/main.nf -params-file params.yaml -c nextflow.config -c cellranger-genomes.config