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Commit f8555ebe authored by Ruben Vorderman's avatar Ruben Vorderman
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solved memory issues

parent 75c5deaf
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2 merge requests!9Changes for virus assembly pipeline,!10Extra tasks required for assembly.
...@@ -6,7 +6,7 @@ task mem { ...@@ -6,7 +6,7 @@ task mem {
String? outputFile = "aligned.bam" String? outputFile = "aligned.bam"
String? preCommand String? preCommand
Int? threads = 1 Int? threads = 1
String? memory = "4G" Int? memory = 4
Int? minimumSeedLength Int? minimumSeedLength
Int? w Int? w
Int? d Int? d
......
...@@ -6,7 +6,7 @@ task cutadapt { ...@@ -6,7 +6,7 @@ task cutadapt {
String? format String? format
String? preCommand String? preCommand
Int? cores = 1 Int? cores = 1
String? memory = "4G" Int? memory = 4
Array[String]+? adapter Array[String]+? adapter
Array[String]+? front Array[String]+? front
Array[String]+? anywhere Array[String]+? anywhere
...@@ -122,4 +122,4 @@ task cutadapt { ...@@ -122,4 +122,4 @@ task cutadapt {
cpu: select_first([cores]) cpu: select_first([cores])
memory: select_first([memory]) memory: select_first([memory])
} }
} }
\ No newline at end of file
...@@ -74,6 +74,6 @@ task spades { ...@@ -74,6 +74,6 @@ task spades {
} }
runtime { runtime {
cpu: select_first([threads]) cpu: select_first([threads])
memory: select_first([memoryGb]) + "G" memory: select_first([memoryGb])
} }
} }
\ No newline at end of file
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