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Complete check_max() move to global config

This commit is contained in:
Bruno Grande 2022-06-23 10:10:28 -07:00
parent a19d79f6ff
commit 6f0d9e6c43
6 changed files with 2 additions and 47 deletions

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@ -202,7 +202,6 @@ Currently documentation is available for the following pipelines within specific
- [MUNIN](docs/pipeline/rnavar/munin.md)
- sarek
- [MUNIN](docs/pipeline/sarek/munin.md)
- [SAGE BIONETWORKS](docs/pipeline/sarek/sage.md)
- [UPPMAX](docs/pipeline/sarek/uppmax.md)
- taxprofiler
- [EVA](docs/pipeline/taxprofiler/eva.md)

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@ -1,37 +0,0 @@
params {
config_profile_description = 'The Sage Bionetworks profile'
config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)'
config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows'
}
// Function to ensure that resource requirements don't go beyond a maximum limit
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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@ -67,7 +67,7 @@ def slow(attempt, factor = 2) {
// Function to ensure that resource requirements don't go
// beyond a maximum limit
// beyond a maximum limit (copied here for Sarek v2)
def check_max(obj, type) {
if (type == 'memory') {
try {

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@ -1,7 +0,0 @@
# nf-core/configs: Sage Bionetworks Sarek-Specific Configuration
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.
In addition to the global configuration described [here](../../sage.md), this Sarek-specific configuration includes the following tweaks:
- Define the `check_max()` function, which is missing in Sarek v2.

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@ -9,6 +9,7 @@ This global configuration includes the following tweaks:
- Enable retries by default when exit codes relate to insufficient memory
- Allow pending jobs to finish if the number of retries are exhausted
- 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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@ -15,5 +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 "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
sage { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/sage.config" }
}