diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index cf9a9ea..9d2a7e1 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -472,4 +472,34 @@ profiles { bwaalnl = 16500 } } + 1240k { + params { + // Specific nf-core/configs params + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs' + } + + executor { + queueSize = 6 + } + + process { + + beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + + maxRetries = 2 + + // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } + + // Increasing walltime for bwa to avoid unnecessary retries + withName:bwa { + time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 72.h : 48.h } + } + + withName:markduplicates { + memory = { task.attempt == 3 ? 16.GB : task.attempt == 2 ? 8.GB : 4.GB } + } + } + } }