Document RSeQC inner_distance limitation for large chromosomes

CHANGELOG.md

@@ -17,6 +17,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
 - [PR #1618](https://github.com/nf-core/rnaseq/pull/1618) - Fix CI: Ensure confirm-pass job runs for markdown-only PRs
 - [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
+- [PR #1624](https://github.com/nf-core/rnaseq/pull/1624) - Document RSeQC inner_distance limitation for genomes with large chromosomes (>500 Mb), such as plant genomes
 - [PR #1620](https://github.com/nf-core/rnaseq/pull/1620) - Fix bigwig strand labeling for reverse-stranded libraries ([#1591](https://github.com/nf-core/rnaseq/issues/1591))
 - [PR #1621](https://github.com/nf-core/rnaseq/pull/1621) - Optimize qualimap performance with multi-threaded name sorting
 

docs/usage.md

@@ -378,6 +378,23 @@ This pipeline uses featureCounts to generate QC metrics based on [biotype](http:
 
 Please get in touch with us on the #rnaseq channel in the [nf-core Slack workspace](https://nf-co.re/join) if you are having problems or need any advice.
 
+#### Large chromosomes (plant genomes)
+
+Genomes with very large chromosomes (>500 Mb), such as plant genomes, may encounter failures in the RSeQC `inner_distance` module due to a known limitation in the underlying bx-python library. The bx-python BitSet implementation has a maximum capacity of approximately 537 million bases, which can be exceeded by chromosomes in organisms like wheat, barley, and other plants.
+
+If you encounter an error message similar to `IndexError: [coordinate] is larger than the size of this BitSet (536870912)`, you can work around this by excluding the `inner_distance` module from RSeQC analysis:
+
+```bash
+--rseqc_modules 'bam_stat,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'
+```
+
+This removes `inner_distance` from the default list of RSeQC modules while retaining all other quality control metrics. Note that the inner_distance metric is only relevant for paired-end data and provides information about fragment size distribution.
+
+For more information, see the upstream issues:
+
+- [nf-core/rnaseq#608](https://github.com/nf-core/rnaseq/issues/608)
+- [bxlab/bx-python#67](https://github.com/bxlab/bx-python/issues/67)
+
 ### iGenomes (not recommended)
 
 If the `--genome` parameter is provided (e.g. `--genome GRCh37`) then the FASTA and GTF files (and existing indices) will be automatically obtained from AWS-iGenomes unless these have already been downloaded locally in the path specified by `--igenomes_base`.