Switching test to use samplesheet.json

assets/samplesheet.json

@@ -0,0 +1,16 @@
+[
+    {
+        "sample": "SAMPLE1",
+        "fastq_1": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz",
+        "fastq_2": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz"
+    },
+    {
+        "sample": "SAMPLE2",
+        "fastq_1": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz",
+        "fastq_2": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz"
+    },
+    {
+        "sample": "SAMPLE3",
+        "fastq_1": "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz"
+    }
+]

nextflow_schema.json

@@ -17,7 +17,7 @@
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|json)$",
                     "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",

tests/default.nf.test

@@ -7,6 +7,7 @@ nextflow_pipeline {
     test("-profile test") {
         when {
             params {
+                input  = "${projectDir}/assets/samplesheet.json"
                 outdir = "$outputDir"
             }
         }