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Merge pull request #393 from Sage-Bionetworks-Workflows/bgrande/sage-sarek-config

Include `check_max()` definition for Sage configuration
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Maxime U. Garcia 2022-06-23 21:47:17 +02:00 committed by GitHub
commit 23669d2df6
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4 changed files with 44 additions and 8 deletions

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@ -10,7 +10,6 @@ A repository for hosting Nextflow configuration files containing custom paramete
- [Configuration and parameters](#configuration-and-parameters)
- [Offline usage](#offline-usage)
- [Adding a new config](#adding-a-new-config)
- [Checking user hostnames](#checking-user-hostnames)
- [Testing](#testing)
- [Documentation](#documentation)
- [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)

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@ -64,3 +64,37 @@ params {
def slow(attempt, factor = 2) {
return Math.ceil( attempt / factor) as int
}
// Function to ensure that resource requirements don't go
// beyond a maximum limit (copied here for Sarek v2)
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}

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@ -1,12 +1,15 @@
# nf-core/configs: Sage Bionetworks Configuration
# nf-core/configs: Sage Bionetworks Global Configuration
To use this custom configuration, run the pipeline with `-profile sage`. This will download and launch the [`sage.config`](../conf/sage.config), which contains a number of optimizations relevant to Sage employees running workflows on AWS (_e.g._ using Nextflow Tower). These include:
To use this custom configuration, run the pipeline with `-profile sage`. This will download and load the [`sage.config`](../conf/sage.config), which contains a number of optimizations relevant to Sage employees running workflows on AWS (_e.g._ using Nextflow Tower). This profile will also load any applicable pipeline-specific configuration.
- Updating the default value for `igenomes_base` to `s3://sage-igenomes`
- Increasing the default time limits because we run pipelines on AWS
- Enabling retries by default when exit codes relate to insufficient memory
This global configuration includes the following tweaks:
- Update the default value for `igenomes_base` to `s3://sage-igenomes`
- Increase the default time limits because we run pipelines on AWS
- Enable retries by default when exit codes relate to insufficient memory
- Allow pending jobs to finish if the number of retries are exhausted
- Slowing the increase in the number of allocated CPU cores on retries
- Slow the increase in the number of allocated CPU cores on retries
- Define the `check_max()` function, which is missing in Sarek v2
## Additional information about iGenomes

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@ -15,4 +15,4 @@ profiles {
cfc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
cfc_dev { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
}
}