From 8c64601f89f9349d8b056f2e29e50ec7ce1a87a7 Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 12 Nov 2024 16:36:07 +0000
Subject: [PATCH 1/4] update docs

---
 docs/usage.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 46fbe6eb..3549542a 100644
--- a/docs/usage.md
+++ b/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 rather than `pri`. 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

From b1513c60bfadc0c973db578dfe3166181a9085e4 Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 12 Nov 2024 16:36:15 +0000
Subject: [PATCH 2/4] update changelog

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae8fdc78..e2ee8bc3 100644
--- a/CHANGELOG.md
+++ b/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/issues/482) - Update documentation regarding MirgeneDB input files.
 
 ## v2.4.0 - 2024-10-14 - Navy Iron Boxer
 

From d04cc55b2b1e8b67edcf801d23908aaf58b9392a Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 12 Nov 2024 16:38:52 +0000
Subject: [PATCH 3/4] fix changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e2ee8bc3..f25e7a40 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## Dev vTBD - TBD - TBD
 
 - [[#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/issues/482) - Update documentation regarding MirgeneDB input files.
+- [[#482]](https://github.com/nf-core/smrnaseq/pull/482) - Update documentation regarding MirgeneDB input files.
 
 ## v2.4.0 - 2024-10-14 - Navy Iron Boxer
 

From 181039afdf80abb1ebc808908e2cf07935b85992 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 12 Nov 2024 14:43:08 -0300
Subject: [PATCH 4/4] Update docs/usage.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com>
---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 3549542a..c525e7b4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -47,7 +47,7 @@ If MirGeneDB should be used instead it needs to be specified using `--mirgenedb`
 
 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 rather than `pri`. 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.
+> [!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