diff --git a/scala/qscript/chartl/private_mutations.q b/scala/qscript/chartl/private_mutations.q index 890bec937..0896d0873 100755 --- a/scala/qscript/chartl/private_mutations.q +++ b/scala/qscript/chartl/private_mutations.q @@ -365,6 +365,8 @@ class private_mutations extends QScript { var inSample = sample @Output(doc="foo") var outList = oList + @Input(doc = "foo") + var waitForMe: File = _ def commandLine = { "grep %s /humgen/1kg/processing/allPopulations_wholeGenome_august_release/bamLists/*.list | tr ':' '\\t' | awk '{print $2}' > %s".format( @@ -383,6 +385,7 @@ class private_mutations extends QScript { add(sites) var bamList : GetBamList = new GetBamList(s,new File(SCRATCH_DIR+"%s.bams.list".format(s))) + bamList.waitForMe = sites.out_list add(bamList)