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Commit 0b157958 authored by Ruben Vorderman's avatar Ruben Vorderman
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also give index

parent 5f7c9945
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2 merge requests!9Changes for virus assembly pipeline,!10Extra tasks required for assembly.
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...@@ -88,7 +88,8 @@ task mem { ...@@ -88,7 +88,8 @@ task mem {
INPUT=/dev/stdin SORT_ORDER=coordinate OUTPUT=${outputFile} INPUT=/dev/stdin SORT_ORDER=coordinate OUTPUT=${outputFile}
} }
output { output {
File alignedFile = select_first([outputFile]) File bamFile = select_first([outputFile])
File bamIndex = sub(bamFile, ".bam$", ".bai")
} }
runtime { runtime {
cpu: select_first([threads]) cpu: select_first([threads])
......
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