From febcbfc05719d28e0c43b385322517f194c335c5 Mon Sep 17 00:00:00 2001
From: Mahwash Jamy <mahwashjamy@gmail.com>
Date: Mon, 31 Oct 2022 16:07:53 +0000
Subject: [PATCH] add missing parameters to nextflow.config

---
 conf/modules.config | 3 ++-
 nextflow.config     | 5 +++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 8e36c5a..eaa5157 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -335,7 +335,8 @@ process {
 
     withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        // one run with multiple samples, so fix ID to just db name to ensure clean log name
+        ext.prefix = { "${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
             mode: params.publish_dir_mode,
diff --git a/nextflow.config b/nextflow.config
index b369f31..6223db0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -118,6 +118,11 @@ params {
     kraken2_save_readclassification = false // added directly to module in profiling.nf
     kraken2_save_minimizers         = false
 
+    //krakenuniq
+    run_krakenuniq                      = false
+    krakenuniq_save_reads               = false // added directly to module in profiling.nf
+    krakenuniq_save_readclassifications = false // added directly to module in profiling.nf
+
     // Bracken
     run_bracken = false