From 1fc80f4274f24ed0a0000f0c23da65d0d013525b Mon Sep 17 00:00:00 2001
From: Matteo Bonfanti <mat.bonfanti@gmail.com>
Date: Fri, 23 Jan 2026 22:56:20 +0100
Subject: [PATCH 1/2] Test pull request by adding a line in README

Added a line to test the pull request functionality.
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index f264dc4..d376900 100644
--- a/README.md
+++ b/README.md
@@ -15,6 +15,7 @@
 ## Introduction
 
 **nfdata-omics/pseudoalign** is a bioinformatics pipeline that ...
+I am adding this line to check what happens with the PR
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the

From b94a0f6c57917a454b694de9c6ee6dc5e8d96d28 Mon Sep 17 00:00:00 2001
From: Matteo Bonfanti <mat.bonfanti@gmail.com>
Date: Fri, 23 Jan 2026 23:09:10 +0100
Subject: [PATCH 2/2] Update comments for clarity in PSEUDOALIGN workflow

---
 workflows/pseudoalign.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/pseudoalign.nf b/workflows/pseudoalign.nf
index a1500eb..91fc982 100644
--- a/workflows/pseudoalign.nf
+++ b/workflows/pseudoalign.nf
@@ -21,10 +21,10 @@ include { UNTAR_SALMON_INDEX     } from '../modules/local/untar_salmon_index/mai
 workflow PSEUDOALIGN {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
-    ch_salmon_index
-    ch_fasta
-    ch_gtf
+    ch_samplesheet   // channel: samplesheet read in from --input
+    ch_salmon_index  // channel: salmon index folder
+    ch_fasta         // channel: transcriptome fasta
+    ch_gtf           // channel: gtf file
 
     main: