From a5f4fc42d53fce99863a3d135b017b9e468722be Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 12 Apr 2022 09:25:27 +0200
Subject: [PATCH] Fix run merging for unmerged PE data

---
 conf/modules.config      | 2 +-
 workflows/taxprofiler.nf | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 97e9510..eb448bb 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -162,7 +162,7 @@ process {
     }
 
     withName: CAT_FASTQ {
-        ext.prefix = { "${meta.id}-${meta.run_accession}" }
+        ext.prefix = { "${meta.id}" }
         publishDir = [
             path: { "${params.outdir}/run_merging/" },
             mode: params.publish_dir_mode,
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 1da812d..2eb7e8c 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -139,7 +139,11 @@ workflow TAXPROFILER {
                     meta_new.remove('run_accession')
                     [ meta_new, reads ]
             }
-            .groupTuple()
+            .groupTuple(by: 0)
+            .map {
+                meta, reads ->
+                    [ meta, reads.flatten() ]
+            }
             .branch {
                 // we can't concate files if there is not a second run, we branch
                 // here to separate them out, and mix after
@@ -151,7 +155,6 @@ workflow TAXPROFILER {
             .mix( ch_reads_for_cat_branch.skip )
             .map {
                 meta, reads ->
-
                 [ meta, [ reads ].flatten() ]
             }