refactor tests

Author: priesgo

Makefile

@@ -5,7 +5,7 @@ all : clean test
 
 clean:
 	rm -rf output
-	#rm -rf work
+	rm -rf work
 	rm -f report.html*
 	rm -f timeline.html*
 	rm -f trace.txt*
@@ -14,14 +14,14 @@ clean:
 	rm -rf .nextflow*
 
 test:
-	bash tests/run_test_0.sh
-	bash tests/run_test_1.sh
-	bash tests/run_test_2.sh
-	bash tests/run_test_3.sh
-	bash tests/run_test_4.sh
-	bash tests/run_test_5.sh
-	bash tests/run_test_6.sh
-	bash tests/run_test_7.sh
-	bash tests/run_test_8.sh
-	bash tests/run_test_10.sh
-	bash tests/run_test_11.sh
+	bash test/scripts/run_test_0.sh
+	bash test/scripts/run_test_1.sh
+	bash test/scripts/run_test_2.sh
+	bash test/scripts/run_test_3.sh
+	bash test/scripts/run_test_4.sh
+	bash test/scripts/run_test_5.sh
+	bash test/scripts/run_test_6.sh
+	bash test/scripts/run_test_7.sh
+	bash test/scripts/run_test_8.sh
+	bash test/scripts/run_test_10.sh
+	bash test/scripts/run_test_11.sh

nextflow.config

@@ -8,8 +8,8 @@ profiles {
   conda { params.enable_conda = true }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {
-    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
-    params.input_vcfs = "$baseDir/test_data/test_input.txt"
+    params.reference = "$baseDir/test/data/ucsc.hg19.minimal.fasta"
+    params.input_vcfs = "$baseDir/test/data/test_input.txt"
     params.cpus = 1
     params.memory = "3g"
     timeline.enabled = false