Fix Samtools indexing for large reference genomes

[apeltzer]

This addresses #146 , where the contig sizes are too long for the regular BAI indices used in the default samtools index process. x-ref https://www.biostars.org/p/111984/ it doesn't really harm to use CSI indices, so I just use these now everywhere instead, which should work both on smaller and larger reference genomes without issues 👍

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[jfy133]

See my comment on #146 (comment)