Skip to content

Fix picard heapspace error in align rule

van den Berg requested to merge hotfix-2019-07-17 into master

In the Singularity image for picard, the default heapsize is too small, leading to crashes in the pipeline when the rule 'align' runs out of heap space. The solution is to explicitly specify the heap space that picard can use, thereby overriding the default value that is set in the Singularity image.

This issue was reported on capture-lumc-wrapper, see for details.

This change was first implemented locally for 20190715W19_11131serie114WESbatch46, since that contained several 'SPOED' samples. This analysis ran successfully.

Merge request reports