From 4f62f5f76b6bafd7de4be44dfc8d86344859f747 Mon Sep 17 00:00:00 2001
From: lconde-ucl <l.conde@ucl.ac.uk>
Date: Mon, 14 Jul 2025 11:17:10 +0100
Subject: [PATCH] Fix PEKA module input mismatch by joining peaks and
 crosslinks on metadata

---
 main.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 7bb5e8e..42d943a 100644
--- a/main.nf
+++ b/main.nf
@@ -543,9 +543,11 @@ workflow CLIPSEQ {
         /*
         * MODULE: Run peka on genome-level crosslinks
         */
+        ch_peka_input = CLIPPY_GENOME.out.peaks
+            .join(ch_genome_crosslink_bed, by: 0)
         PEKA (
-            CLIPPY_GENOME.out.peaks,
-            ch_genome_crosslink_bed,
+            ch_peka_input.map { meta, peaks, crosslinks -> [meta, peaks] },
+            ch_peka_input.map { meta, peaks, crosslinks -> [meta, crosslinks] },
             ch_fasta.collect{ it[1] },
             ch_fasta_fai.collect{ it[1] },
             ch_regions_resolved_gtf.collect{ it[1] }