From 8254e5bc43ffc46aa300bb4db3d0d410e8a60164 Mon Sep 17 00:00:00 2001
From: Thomieh73 <Thhaverk@gmail.com>
Date: Fri, 15 Mar 2024 13:52:52 +0100
Subject: [PATCH] corrected the EMU modules and made sure that the workflow now
 can run with amplicons

---
 modules/EMU.nf | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/modules/EMU.nf b/modules/EMU.nf
index 5000b40..15be143 100644
--- a/modules/EMU.nf
+++ b/modules/EMU.nf
@@ -32,7 +32,7 @@ process EMU_CLASS {
         --threads 20 \
         *.fastq.gz
 
-	ln -s ${samplename}.emu/${samplename}.clean_rel-abundance.tsv ./
+	ln -s ${samplename}.emu/${samplename}.nfilt.fastq_rel-abundance.tsv ./${samplename}.rel-abundance.tsv
 
 	"""
 }
@@ -64,11 +64,8 @@ process EMU_COMBINE {
 	script:
 	samplename = x.toString() - ~/.nfilt.fastq.gz$/
 	"""
-	ls -la
-  	for taxon in species genus family order class phylum clade superkingdom; do
-		 echo running $taxon
-		 emu combine-outputs combined_output $taxon
-	done
+	ls
+  	for taxon in species genus family order class phylum superkingdom; do echo running \$taxon ; emu combine-outputs ./ \$taxon ; done
 
 	"""
 }
\ No newline at end of file