Expand tests and fix schema after review

.github/workflows/ci.yml

@@ -29,8 +29,16 @@ jobs:
           - NXF_VER: ""
             NXF_EDGE: "1"
         parameters:
+          - "--longread_clip false"
+          - "--shortread_clip false"
           - "--shortread_clipmerge_tool fastp"
+          - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
+          - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
           - "--shortread_clipmerge_tool adapterremoval"
+          - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
+          - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
+          - "--shortread_complexityfilter_tool bbduk"
+          - "--shortread_complexityfilter_tool prinseq"
 
     steps:
       - name: Check out pipeline code

conf/test.config

@@ -28,5 +28,6 @@ params {
     run_malt                      = true
     run_metaphlan3                = true
     shortread_clipmerge           = true
+    longread_clip                 = false
     shortread_complexityfilter    = true
 }

nextflow.config

@@ -51,7 +51,7 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
-    // Databaess
+    // Databases
     databases = null
 
     // FASTQ preprocessing

nextflow_schema.json

@@ -328,7 +328,8 @@
         },
         "shortread_complexityfilter_prinseqplusplus_mode": {
             "type": "string",
-            "default": "entropy"
+            "default": "entropy",
+            "enum": ["entropy", "dust"]
         },
         "shortread_complexityfilter_prinseqplusplus_dustscore": {
             "type": "number",