Fix indenting of nextflow.config

nextflow.config

@@ -1,6 +1,6 @@
 // Workflow details
 manifest {
-    author              = 'Sydney Informatics Hub, University of Sydney'
+    author              = 'Georgie Samaha, Sydney Informatics Hub, University of Sydney'
     name                = 'GermlineStructuralV-nf'
     description         = 'Multi-caller germline structural variant calling pipeline'
     homePage            = 'https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf'
@@ -11,27 +11,27 @@ nextflowVersion     = '!>=20.07.1'
 
 // Set default parameters
 params {
-  version	          = '1.0'
-  help		          = false
-  input		          = false
-  ref		            = false
-  intervals	        = false
-  outDir		        = './results'
-  survivorMaxDist	  = 1000
-  survivorConsensus = 1
-  survivorType	    = 1
-  survivorStrand	  = 1
-  survivorSize	    = 40
-  annotsvDir	      = false
-  annotsvMode	      = 'both'
-  extraMantaFlags   = false
-  extraSmooveFlags  = false
-  extraTidditCovFlags = false
-  extraTidditSvFlags= false
-  extraAnnotsvFlags = false
-  pbs_account       = false
-  slurm_account     = false
-  whoami            = false
+  version	          	= '1.0'
+  help		          	= false
+  input		          	= null
+  ref		          		= false
+  intervals	        	= false
+  outDir		        	= './results'
+  survivorMaxDist	  	= 1000
+  survivorConsensus 	= 1
+  survivorType	    	= 1
+  survivorStrand	  	= 1
+  survivorSize	    	= 40
+  annotsvDir	      	= false
+  annotsvMode	      	= 'both'
+  extraMantaFlags   	= false
+  extraSmooveFlags  	= false
+  extraTidditCovFlags	= false
+  extraTidditSvFlags	= false
+  extraAnnotsvFlags 	= false
+  pbs_account       	= false
+  slurm_account     	= false
+  whoami            	= false
 }
 
 // Preset use of containers with Singularity
@@ -114,25 +114,25 @@ withName: 'annotsv' {
 def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 
 // Produce a workflow diagram
-  dag {
-    enabled = true
-    file = "${params.outDir}/runInfo/GermlineStructuralV_dag_${timestamp}.svg"
-  }
+dag {
+  enabled = true
+  file = "${params.outDir}/runInfo/GermlineStructuralV_dag_${timestamp}.svg"
+}
 
-  report {
-    enabled = true
-    file = "${params.outDir}/runInfo/GermlineStructuralV_report_${timestamp}.html"
-  }
+report {
+  enabled = true
+  file = "${params.outDir}/runInfo/GermlineStructuralV_report_${timestamp}.html"
+}
 
-  timeline {
-    enabled = true
-    overwrite = true
-    file = "${params.outDir}/runInfo/GermlineStructuralV_timeline_${timestamp}.html"
-  }
+timeline {
+  enabled = true
+	overwrite = true
+	file = "${params.outDir}/runInfo/GermlineStructuralV_timeline_${timestamp}.html"
+}
 
-  trace {
-    enabled = true
-    overwrite = true
-    file = "${params.outDir}/runInfo/GermlineStructuralV_trace_${timestamp}.txt"
-    fields = 'process,name,status,queue,realtime,cpus,%cpu,memory,%mem,rss,env'
-  }
+trace {
+	enabled = true
+	overwrite = true
+  file = "${params.outDir}/runInfo/GermlineStructuralV_trace_${timestamp}.txt"
+  fields = 'process,name,status,queue,realtime,cpus,%cpu,memory,%mem,rss,env'
+}