Fix validation schema, and fix assembly channels for longread and sho…

…rtread assemblers, when assembly input is given
nf-core · Nov 29, 2024 · 75a36f2 · 75a36f2
1 parent e277290
commit 75a36f2
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Showing 2 changed files with 5 additions and 20 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -43,26 +43,7 @@
             }
         },
         "required": ["sample", "group"],
-        "allOf": [
-            {
-                "if": {
-                    "required": ["short_reads_2"]
-                },
-                "then": {
-                    "required": ["short_reads_1"]
-                }
-            },
-            {
-                "if": {
-                    "not": {
-                        "allOf": [{ "required": ["short_reads_1"] }, { "required": ["short_reads_2"] }]
-                    }
-                },
-                "then": {
-                    "required": ["long_reads"]
-                }
-            }
-        ]
+        "anyOf": [{ "required": ["short_reads_1"] }, { "required": ["long_reads"] }]
     },
     "uniqueEntries": ["sample", "run"],
     "dependentRequired": {

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -616,6 +616,10 @@ workflow MAG {
 
         ch_assemblies = Channel.empty()
         ch_assemblies = ch_assemblies.mix(ch_assemblies_split.ungzip, GUNZIP_ASSEMBLYINPUT.out.gunzip)
+        ch_shortread_assemblies = Channel.empty()
+        ch_shortread_assemblies = ch_shortread_assemblies.mix(ch_assemblies_split.ungzip, GUNZIP_ASSEMBLYINPUT.out.gunzip)
+        // TODO ALSO FIX FOR LONGREAD
+        ch_longread_assemblies = Channel.empty()
     }
 
     ch_quast_multiqc = Channel.empty()