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Commit bf614579 authored by Ruben Vorderman's avatar Ruben Vorderman
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try to fix memory

parent 6d737097
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......@@ -104,7 +104,9 @@ task Star {
Int runThreadN = 4
# Use a margin of 30% index size. Real memory usage is ~30 GiB for a 27 GiB index.
Int memoryGb = 1 + ceil(size(indexFiles, "G") * 1.3)
String memory = "~{memoryGb}G"
# For some reason doing above calculation inside a string does not work.
# So we solve it with an optional memory string and using select_first.
String? memory
# 1 minute initialization + time reading in index (1 minute per G) + time aligning data.
Int timeMinutes = 1 + ceil(size(indexFiles, "G")) + ceil(size(flatten([inputR1, inputR2]), "G") * 180 / runThreadN)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
......@@ -137,7 +139,7 @@ task Star {
runtime {
cpu: runThreadN
memory: memory
memory: select_first([memory, "~{memoryGb}G"])
time_minutes: timeMinutes
docker: dockerImage
}
......
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