Configure initial parameters for running the pipeline

insilicodb.config

@@ -1,12 +1,69 @@
 {
   "parameters":
-    "fastaFile": {
-         "description": "The FASTA file to take as input to kallisto"
-     },
-    "fastqFile1":{
-        "description": "The first fastq file"
-     },
-    "fastqFile2": {
-         "description": "The second fastq file"
-    } 
+
+    "test-text": {
+        "type": "string",
+        "description": "a test to validate strings"
+    },
+
+    // index
+
+    "index.kmer-size": {
+        "type": "integer",
+        "description": "k-mer (odd) length (default: 31, max value: 31)"
+    },
+    "index.make-unique": {
+        "type": "boolean",
+        "description": "Replace repeated target names with unique names"
+    }
+    "index.files": {
+        "type": "files",
+        "description": "FASTA files",
+        "required": true
+    },
+
+
+    // quant
+
+    "quant.index": {
+        "type": "file",
+        "description": "Filename for the kallisto index to be used for quantification"
+    },
+    "quant.files": {
+        "type": "files",
+        "description": "FASTQ files",
+        "required": true
+    },
+    "quant.bias": {
+        "type": "boolean",
+        "description": "Perform sequence based bias correction"
+    },
+    "quant.bootstrap-samples": {
+        "type": "integer",
+        "description": "Number of bootstrap samples (default: 0)"
+    },
+    "quant.seed": {
+        "type": "integer",
+        "description": "Seed for the bootstrap sampling (default: 42)"
+    },
+    "quant.single": {
+        "type": "boolean",
+        "description": "Quantify single-end reads"
+    },
+    "quant.fragment-length": {
+        "type": "double",
+        "description": "Estimated average fragment length"
+    },
+    "quant.standard-deviation": {
+        "type": "double",
+        "description": "Estimated standard deviation of fragment length (default: value is estimated from the input data)"
+    },
+    "quant.threads": {
+        "type": "integer",
+        "description": "Number of threads to use (default: 1)"
+    },
+    "quant.pseudobam": {
+        "type": "boolean",
+        "description": "Output pseudoalignments in SAM format to stdout"
+    }
 }