diff --git a/conf/eddie.config b/conf/eddie.config new file mode 100644 index 0000000..11ae1d9 --- /dev/null +++ b/conf/eddie.config @@ -0,0 +1,30 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'University of Edinburgh (eddie) cluster profile provided by nf-core/configs.' + config_profile_contact = 'Alison Meynert (@ameynert)' + config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing' +} + +conda.createTimeout = '2h' + +process { + executor = 'sge' + + # memory environment & options + clusterOptions = {"-l h_vmem=${task.memory.bytes/task.cpus}"} + penv = 'sharedmem' + + # common SGE error statuses + errorStrategy = {task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish'} + maxErrors = '-1' + maxRetries = 3 + + # load module script for Anaconda + beforeScript = { '. /etc/profile.d/modules.sh; sleep 2; ' } + module = 'anaconda/5.3.1' +} +params { + saveReference = true + // illumina iGenomes reference file paths on GIS Aquila + igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes/' +}