Use CSI indexes for BAMs instead of BAI indexes.

[afonsoguerra]

While running the dev version of this pipeline I managed to produce a large contig. This produced error:

  [E::hts_idx_check_range] Region 536854800..536872065 cannot be stored in a bai index. Try using a csi index

As such, this PR aims to replace the default bai index with a csi index to avoid this error.

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• CHANGELOG.md is updated. (this is not a full release so I did not update changeling)
• README.md is updated (including new tool citations and authors/contributors). (not sure this merits any change to the readme either)

[nschan]

Thank you for opening this PR, I will see how I can best align this with #171 .

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[nschan]

I think your latest commit is far outside the scope of this PR.
Please open a new PR for these larger changes. While I truly appreciate contributions to this, as mentioned above, the pipeline is currently undergoing a major refactor (#171) and these additions are likely not going to work with the changes I implemented. I am happy to discuss how to align your work with the upcoming changes in a separate PR.

[afonsoguerra]

Sorry, it was my mistake. I've reverted it now. I am just trying to get this pipeline work for my needs, but once I'm done with it and feel it is stable I will obviously get in touch and let you pick and choose what functionality is useful to a broader user base and will submit PRs then. Keep up the good work with the refactoring!

[nschan]

Hi,

it took me a while to find the time to finally merge #171, but pipeline dev is now refactored. It should now use csi indices, and has an option to adjust index size via params.csi_index_size.
If you would have some time to take a look if this is ok, or if there were things in this PR that I missed, please let me know @afonsoguerra. If everything is ok, please close this PR.