Exclude parameters.

workflows/casava_qc/workflow.properties

@@ -34,17 +34,21 @@ description = casava 1.8 quality check pipeline
 casava_directory.name = casava_directory
 casava_directory.flag = --casava-directory
 casava_directory.help = Where are stored casava results (see also lane-number)
-casava_directory.required = False
+casava_directory.required = True
+casava_directory.exclude = read_1
 
 lane_number.name = lane_number
 lane_number.flag = --lane-number
 lane_number.help = Which lane should be processed (mandatory with casava-directory)
-lane_number.required = False
+lane_number.required = True
+lane_number.exclude = read_1
 
 read_1.name = read_1
 read_1.flag = --read-1
 read_1.help = Which read1 files should be used
 read_1.action = append
+read_1.required = True
+read_1.exclude = casava_directory
 
 read_2.name = read_2
 read_2.flag = --read-2

workflows/illumina_qc/workflow.properties

@@ -34,17 +34,21 @@ description = illumina quality check pipeline
 casava_directory.name = casava_directory
 casava_directory.flag = --casava-directory
 casava_directory.help = Where are stored casava results (see also lane-number)
-casava_directory.required = False
+casava_directory.required = True
+casava_directory.exclude = read_1
 
 lane_number.name = lane_number
 lane_number.flag = --lane-number
 lane_number.help = Which lane should be processed (mandatory with casava-directory)
-lane_number.required = False
+lane_number.required = True
+lane_number.exclude = read_1
 
 read_1.name = read_1
 read_1.flag = --read-1
 read_1.help = Which read1 files should be used
 read_1.action = append
+read_1.required = True
+read_1.exclude = casava_directory
 
 read_2.name = read_2
 read_2.flag = --read-2

workflows/illumina_rnaseq/workflow.properties

@@ -34,15 +34,21 @@ description = rnaseq quality check pipeline
 casava_directory.name = casava_directory
 casava_directory.flag = --casava-directory
 casava_directory.help = Where are stored casava results (see also lane-number)
+casava_directory.required = True
+casava_directory.exclude = read_1
 
 lane_number.name = lane_number
 lane_number.flag = --lane-number
 lane_number.help = Which lane should be processed (mandatory with casava-directory)
+lane_number.required = True
+lane_number.exclude = read_1
 
 read_1.name = read_1
 read_1.flag = --read-1
 read_1.help = Which read1 files should be used
 read_1.action = append
+read_1.required = True
+read_1.exclude = casava_directory
 
 read_2.name = read_2
 read_2.flag = --read-2