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

[nick-youngblut]

This pull request includes updates to the documentation and schema to clarify the usage of the cellranger_index parameter. The changes ensure that users provide the correct base directory path for the index.

Documentation updates:

• docs/usage.md: Updated the description of the --cellranger_index parameter to specify that users should provide the base path of the index and included an example path.

Schema updates:

• nextflow_schema.json: Modified the description of the cellranger_index property to include an example path and clarify that the base directory of the index should be provided.

PR checklist

• This comment contains a description of changes (with reason).
• [N/A] If you've fixed a bug or added code that should be tested, add tests!
• [N/A] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• [N/A] If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• [N/A] CHANGELOG.md is updated.
• [N/A] README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @nick-youngblut,

It looks like this pull-request is has been made against the nick-youngblut/scrnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nick-youngblut/scrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[grst]

@nf-core-bot fix linting