Let users run both annotators, if they really want

viklund · viklund · commit cf5946423245 · 2016-10-04T13:23:09.000+02:00
(It's good for testing too)
diff --git a/main.nf b/main.nf
@@ -448,10 +448,6 @@ def processWorkflowSteps(steps) {
 
     workflowSteps = steps.split(',').collect { it.trim().toLowerCase() }
 
-    if ('vep' in workflowSteps && 'snpeff' in workflowSteps) {
-        exit 1, 'You can only run one annotator, either "vep" or "snpeff"'
-    }
-
     if ('manta' in workflowSteps) {
         workflowSteps.push( 'indexbam' )
     }

Original file line number	Diff line number	Diff line change
`@@ -448,10 +448,6 @@ def processWorkflowSteps(steps) {`
`448`	`448`
`449`	`449`	`workflowSteps = steps.split(',').collect { it.trim().toLowerCase() }`
`450`	`450`
`451`		`- if ('vep' in workflowSteps && 'snpeff' in workflowSteps) {`
`452`		`- exit 1, 'You can only run one annotator, either "vep" or "snpeff"'`
`453`		`- }`
`454`		`-`
`455`	`451`	`if ('manta' in workflowSteps) {`
`456`	`452`	`workflowSteps.push( 'indexbam' )`
`457`	`453`	`}`