tests_succesfull again

Joon-Klaps · Sep 28, 2023 · afc931d · afc931d
1 parent 324f9d0
commit afc931d
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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)