From d46ddd972c2fc2c3ce0e7fe03b3ad42a4821332a Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 5 Apr 2022 11:04:30 +0200
Subject: [PATCH] Expand tests and fix schema after review

---
 .github/workflows/ci.yml |  8 ++++++++
 conf/test.config         | 13 +++++++------
 nextflow.config          |  2 +-
 nextflow_schema.json     |  3 ++-
 4 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b8975b5..79148f0 100644
--- a/.github/workflows/ci.yml
+++ b/.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
diff --git a/conf/test.config b/conf/test.config
index ff92fe7..bdad2c1 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,11 +22,12 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
-    databases           = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
-    run_kraken2         = true
-    run_malt            = true
-    run_metaphlan3      = true
-    shortread_clipmerge = true
+    input                         = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                     = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    run_kraken2                   = true
+    run_malt                      = true
+    run_metaphlan3                = true
+    shortread_clipmerge           = true
+    longread_clip                 = false
     shortread_complexityfilter    = true
 }
diff --git a/nextflow.config b/nextflow.config
index cd81f08..e6d6307 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -51,7 +51,7 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
-    // Databaess
+    // Databases
     databases = null
 
     // FASTQ preprocessing
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bec9ea4..6f6125e 100644
--- a/nextflow_schema.json
+++ b/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",