From afc931da5d35a74f9ae9d0fa6c88ede63ea901b4 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@gmail.com>
Date: Thu, 28 Sep 2023 17:46:55 +0200
Subject: [PATCH] tests_succesfull again

---
 conf/test.config        | 2 +-
 nextflow_schema.json    | 7 ++++++-
 workflows/viralgenie.nf | 5 +----
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 2c631cea..7e3f674a 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     host_genome = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     skip_complexity_filtering   = false
     trim_tool                   ='fastp'
-    assemblers                  ='spades,megahit'
+    assemblers                  ='spades,megahit,trinity'
 
     skip_metagenomic_diversity  = true
     save_databases              = true
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e020f51e..b9848e15 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -480,6 +480,7 @@
                     "fa_icon": "fas fa-bezier-curve",
                     "enum": [
                         "spades,trinity,megahit",
+                        "megahit,trinity,spades",
                         "spades",
                         "trinity",
                         "megahit",
@@ -488,7 +489,11 @@
                         "megahit,spades",
                         "spades,megahit",
                         "trinity,spades",
-                        "spades,trinity"
+                        "spades,trinity",
+                        "spades,megahit,trinity",
+                        "megahit,spades,trinity",
+                        "trinity,spades,megahit",
+                        "trinity,megahit,spades"
                     ],
                     "description": "The specified tools for denovo assembly, multiple options are possible"
                 },
diff --git a/workflows/viralgenie.nf b/workflows/viralgenie.nf
index 2ff08c1d..7b47ca90 100644
--- a/workflows/viralgenie.nf
+++ b/workflows/viralgenie.nf
@@ -154,15 +154,12 @@ workflow VIRALGENIE {
         FASTQ_SPADES_TRINITY_MEGAHIT
             .out
             .scaffolds
-            .branch{ meta, scaffolds,count ->
+            .branch{ meta, scaffolds ->
                 no_contigs: scaffolds.countFasta() == 0
                 any_contigs: scaffolds.countFasta() > 0
             }
             .set{ch_contigs}
 
-        ch_contigs.no_contigs.view()
-        ch_contigs.any_contigs.view()
-
         if (!params.skip_polishing){
             unpacked_references = UNPACK_DB_BLAST (params.reference_fasta).db
             ch_versions         = ch_versions.mix(UNPACK_DB_BLAST.out.versions)