Skip to content
Snippets Groups Projects
Commit dd9990d9 authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

fix spades memory allocation

parent 4c0b9385
No related branches found
No related tags found
1 merge request!11Changes needed for the iterative assembly pipeline
...@@ -28,8 +28,8 @@ task spades { ...@@ -28,8 +28,8 @@ task spades {
Float? covCutoff Float? covCutoff
Int? phredOffset Int? phredOffset
Int finalThreads = select_first([threads,1]) Int finalThreads = select_first([threads,1])
Int totalMemory = select_first([memoryGb, finalThreads * 16]) Float totalMemory = select_first([memoryGb, finalThreads * 16])
Int clusterMemory = totalMemory / finalThreads Int clusterMemory = ceil(totalMemory / finalThreads)
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -57,7 +57,7 @@ task spades { ...@@ -57,7 +57,7 @@ task spades {
${true="--disable-rr" false="" disableRepeatResolution } \ ${true="--disable-rr" false="" disableRepeatResolution } \
${"--dataset " + dataset } \ ${"--dataset " + dataset } \
${"--threads " + finalThreads} \ ${"--threads " + finalThreads} \
${"--memory " + totalMemory } \ ${"--memory " + ceil(totalMemory) } \
${"-k " + k } \ ${"-k " + k } \
${"--cov-cutoff " + covCutoff } \ ${"--cov-cutoff " + covCutoff } \
${"--phred-offset " + phredOffset } ${"--phred-offset " + phredOffset }
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment