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Merge pull request #176 from jfy133/master

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Add new group profile for eager@SHH
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James A. Fellows Yates 2020-08-11 09:24:43 +02:00 committed by GitHub
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12
conf/pipeline/eager/shh.config
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@ -65,6 +65,18 @@ process {
} }
profiles { profiles {
microbiome_screening {
process {
// Assuming NCBI NT-sized DB
withName: malt {
maxRetries = 1
memory = 1900.GB
cpus = 112
time = 1440.h
queue = 'supercruncher'
}
}
}
// IMPORTANT this profile is not reproducible due to hardcoded paths. For initial/automated screening ONLY. // IMPORTANT this profile is not reproducible due to hardcoded paths. For initial/automated screening ONLY.
hops { hops {
params { params {

4
docs/pipeline/eager/shh.md
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@ -20,6 +20,10 @@ Specific configurations for shh has been made for eager.
### Contextual profiles ### Contextual profiles
#### Microbiome Sciences
* `microbiome_screening` runs MALT straight to supercruncher (with no retries!) and full resources requested due to microbiome screening databases often easily reach this size
#### Human Pop-Gen #### Human Pop-Gen
* `human`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16500, -n 0.01`) * `human`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16500, -n 0.01`)