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updated --cellranger_index docs to point out that the base index directory is needed #458

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Merged
merged 3 commits into from
Mar 27, 2025
Merged

updated --cellranger_index docs to point out that the base index directory is needed #458

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23ad77b
updated --cellranger_index docs
nick-youngblut Mar 26, 2025
5ab3ba6
Merge branch 'dev' into cellranger_index_docs_update
nick-youngblut Mar 26, 2025
2aacd64
[automated] Fix code linting
nf-core-bot Mar 27, 2025
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5 changes: 3 additions & 2 deletions docs/usage.md
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Expand Up @@ -139,8 +139,9 @@ test_scARC,path/test_scARC_gex_S1_L002_R1_001.fastq.gz,path/test_scARC_gex_S1_L0

#### Config file and index

Cellranger-arc needs a reference index directory that you can provide with `--cellranger_index`. Be aware, you can use
for cellranger-arc the same index you use for cellranger ([see](https://kb.10xgenomics.com/hc/en-us/articles/4408281606797-Are-the-references-interchangeable-between-pipelines)).
Cellranger-arc needs a reference index directory that you can provide with `--cellranger_index`.
Besure to provide the base path of the index (e.g., `--cellranger_index /PATH/TO/10X_REF/refdata-gex-GRCh38-2024-A/`).
Be aware, you can use for cellranger-arc the same index you use for cellranger ([see](https://kb.10xgenomics.com/hc/en-us/articles/4408281606797-Are-the-references-interchangeable-between-pipelines)).
Yet, a cellranger-arc index might include additional data (e.g., TF binding motifs). Therefore, please first check if
you have to create a new cellranger-arc index ([see here](https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references) for
more information)
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -278,7 +278,7 @@
"properties": {
"cellranger_index": {
"type": "string",
"description": "Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website. ",
"description": "Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website. Provide the base directory of the index (e.g., '/PATH/TO/10X_REF/refdata-gex-GRCh38-2024-A/')",
"format": "path",
"exists": true
},
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