From 3acf993586bbad49ae487babc677791d66d04cca Mon Sep 17 00:00:00 2001
From: Sarah Griffiths <sarah.griffiths@nanoporetech.com>
Date: Fri, 8 Dec 2023 09:32:07 +0000
Subject: [PATCH] de_analysis include in sample cmd

---
 CHANGELOG.md    | 2 ++
 main.nf         | 4 ++--
 nextflow.config | 1 +
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cfe2197..fb760b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Memory requirements for each process.
 ### Changed
 - Documentation.
+### Fixed
+- When Jaffa is run only output one report.
 
 ## [v0.4.2]
 ### Changed
diff --git a/main.nf b/main.nf
index c5e71cd..f0cc532 100644
--- a/main.nf
+++ b/main.nf
@@ -606,8 +606,8 @@ workflow pipeline {
         }
         if (jaffal_refBase){
                 gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
-                jaffal_out = gene_fusions.out.results_csv.collectFile(keepHeader: true, name: 'jaffal.csv')
-            }else{
+                jaffal_out = gene_fusions.out.results_csv.map{ alias, csv -> csv}.collectFile(keepHeader: true, name: 'jaffal.csv')
+            } else{
                 jaffal_out = file("$projectDir/data/OPTIONAL_FILE")
         }
 
diff --git a/nextflow.config b/nextflow.config
index cd9c5dc..1bb98ab 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -98,6 +98,7 @@ params {
         "--minimap2_index_opts '-k15'",
         "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
         "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
+        "--de_analysis",
       ]
     agent = null
     container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"