Updated input schema and used nf-core/modules test data

assets/samplesheet.csv

@@ -1,3 +1,3 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,reads_1,reads_2
+sarscov2_1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz
+sarscov2_2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz

assets/schema_input.json

@@ -19,21 +19,21 @@
                 "errorMessage": "Group ID cannot contain spaces",
                 "meta": ["group"]
             },
-            "fastq_1": {
+            "reads_1": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
-            "fastq_2": {
+            "reads_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "reads_1"]
     }
 }

conf/test.config

@@ -20,6 +20,6 @@ params {
     max_time                    = '6.h'
 
     // Input data
-    input                       = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
+    input                       = 'https://raw.githubusercontent.com/GallVp/prepngs/dev/assets/samplesheet.csv'
     min_trimmed_reads           = 10
 }