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Commit 8ffea620 authored by Ruben Vorderman's avatar Ruben Vorderman
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tweak spades memory

parent a161c72c
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Tags phhv1reassembly
1 merge request!11Changes needed for the iterative assembly pipeline
...@@ -28,7 +28,8 @@ task spades { ...@@ -28,7 +28,8 @@ task spades {
Float? covCutoff Float? covCutoff
Int? phredOffset Int? phredOffset
Int finalThreads = select_first([threads,1]) Int finalThreads = select_first([threads,1])
Float totalMemory = select_first([memoryGb, finalThreads * 16]) Float totalMemory = select_first([memoryGb, finalThreads * 16.0])
Int finalMemory = ceil(totalMemory)
Int clusterMemory = ceil(totalMemory / finalThreads) Int clusterMemory = ceil(totalMemory / finalThreads)
command { command {
...@@ -57,7 +58,7 @@ task spades { ...@@ -57,7 +58,7 @@ task spades {
${true="--disable-rr" false="" disableRepeatResolution } \ ${true="--disable-rr" false="" disableRepeatResolution } \
${"--dataset " + dataset } \ ${"--dataset " + dataset } \
${"--threads " + finalThreads} \ ${"--threads " + finalThreads} \
${"--memory " + ceil(totalMemory) } \ ${"--memory " + finalMemory } \
${"-k " + k } \ ${"-k " + k } \
${"--cov-cutoff " + covCutoff } \ ${"--cov-cutoff " + covCutoff } \
${"--phred-offset " + phredOffset } ${"--phred-offset " + phredOffset }
......
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