Merge pull request #482 from atrigila/add_docs_mirtop

Add docs mirtop

CHANGELOG.md

@@ -5,7 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev vTBD - TBD - TBD
 
-- [[#477]](https://github.com/nf-core/smrnaseq/issues/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
+- [[#481]](https://github.com/nf-core/smrnaseq/pull/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
+- [[#482]](https://github.com/nf-core/smrnaseq/pull/482) - Update documentation regarding MirgeneDB input files.
 
 ## v2.4.0 - 2024-10-14 - Navy Iron Boxer
 

docs/usage.md

@@ -45,6 +45,10 @@ If MirGeneDB should be used instead it needs to be specified using `--mirgenedb`
 - `mirgenedb_mature`: This parameter should point to the FASTA file containing mature miRNA sequences. The file can be manually downloaded from [MirGeneDB](https://mirgenedb.org/download).
 - `mirgenedb_hairpin`: This parameter should point to the FASTA file containing precursor miRNA sequences. Note that MirGeneDB does not offer a dedicated hairpin file, but the precursor sequences can be downloaded from [MirGeneDB](https://mirgenedb.org/download) and used instead.
 
+See examples in: [the test-datasets repository of nf-core](https://github.com/nf-core/test-datasets/tree/smrnaseq/MirGeneDB).
+
+> [!NOTE] > `mirtop` is hard-coded to use the `pre` sequences, which originate from the hairpin FASTA, rather than the `pri` sequences, which come from the mature FASTA. Users must provide `pre` files from the start to ensure consistency between the FASTA and GFF files, as the coordinates in the GFF file are referenced to `pre` sequences. This also ensures that names in the BAM file will match those in the GFF.
+
 ### Genome
 
 - `fasta`: the reference genome FASTA file