Fix merge conflicts

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,6 +10,7 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 

.github/workflows/ci.yml

@@ -36,7 +36,6 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
-
   parameters:
     name: Test workflow parameters
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
@@ -136,4 +135,4 @@ jobs:
 
       - name: Run pipeline with minimal Nanopore data and various options
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }}

lib/NfcoreSchema.groovy

@@ -119,8 +119,14 @@ class NfcoreSchema {
             }
             // unexpected params
             def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
-            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam)) {
-                unexpectedParams.push(specifiedParam)
+            def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
+            def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
+            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !expectedParamsLowerCase.contains(specifiedParamLowerCase)) {
+                // Temporarily remove camelCase/camel-case params #1035
+                def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
+                if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
+                    unexpectedParams.push(specifiedParam)
+                }
             }
         }
 

nextflow.config

@@ -153,7 +153,6 @@ profiles {
     podman.enabled         = false
     shifter.enabled        = false
     charliecloud.enabled   = false
-
   }
   docker {
     docker.enabled         = true

nextflow_schema.json

@@ -685,4 +685,4 @@
             "$ref": "#/definitions/institutional_config_options"
         }
     ]
-}
+}