docs on cellranger_index path

[nick-youngblut]

Description of feature

Current docs:

 --cellranger_index
Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.

It would help to provide an example of what that path should actually look like. For instance, curl -sL https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz | tar -tzf - results in:

refdata-gex-GRCh38-2024-A/
refdata-gex-GRCh38-2024-A/reference.json
refdata-gex-GRCh38-2024-A/star/
refdata-gex-GRCh38-2024-A/star/exonGeTrInfo.tab
refdata-gex-GRCh38-2024-A/star/sjdbInfo.txt
refdata-gex-GRCh38-2024-A/star/chrLength.txt
refdata-gex-GRCh38-2024-A/star/exonInfo.tab
refdata-gex-GRCh38-2024-A/star/Genome
refdata-gex-GRCh38-2024-A/star/chrName.txt
refdata-gex-GRCh38-2024-A/star/chrStart.txt
refdata-gex-GRCh38-2024-A/star/chrNameLength.txt
refdata-gex-GRCh38-2024-A/star/geneInfo.tab
refdata-gex-GRCh38-2024-A/star/transcriptInfo.tab
refdata-gex-GRCh38-2024-A/star/sjdbList.fromGTF.out.tab
refdata-gex-GRCh38-2024-A/star/sjdbList.out.tab
refdata-gex-GRCh38-2024-A/star/genomeParameters.txt
refdata-gex-GRCh38-2024-A/star/SA
refdata-gex-GRCh38-2024-A/star/SAindex
refdata-gex-GRCh38-2024-A/fasta/
refdata-gex-GRCh38-2024-A/fasta/genome.fa.fai
refdata-gex-GRCh38-2024-A/fasta/genome.fa
refdata-gex-GRCh38-2024-A/genes/
refdata-gex-GRCh38-2024-A/genes/genes.gtf.gz

So the user could possibly specify refdata-gex-GRCh38-2024-A/, or refdata-gex-GRCh38-2024-A/star/ or refdata-gex-GRCh38-2024-A/reference.json, etc.

However, unless the user provides, --cellranger_index refdata-gex-GRCh38-2024-A/, they will get the following somewhat cryptic error:

[error] Your reference does not contain the expected files, or they are not readable.

[grst]

Thanks for bringing this up! Do you want to submit a PR to update the docs?

[nick-youngblut]

Yeah, I can submit the PR

[nick-youngblut]

Done: #458