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Complete check_max()
move to global config
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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
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- [MUNIN](docs/pipeline/rnavar/munin.md)
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- sarek
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- [MUNIN](docs/pipeline/sarek/munin.md)
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- [SAGE BIONETWORKS](docs/pipeline/sarek/sage.md)
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- [UPPMAX](docs/pipeline/sarek/uppmax.md)
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- taxprofiler
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- [EVA](docs/pipeline/taxprofiler/eva.md)
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@ -1,37 +0,0 @@
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params {
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config_profile_description = 'The Sage Bionetworks profile'
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config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)'
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config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows'
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}
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// Function to ensure that resource requirements don't go beyond a maximum limit
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min( obj, params.max_cpus as int )
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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}
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}
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}
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@ -67,7 +67,7 @@ def slow(attempt, factor = 2) {
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// Function to ensure that resource requirements don't go
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// beyond a maximum limit
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// beyond a maximum limit (copied here for Sarek v2)
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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@ -1,7 +0,0 @@
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# nf-core/configs: Sage Bionetworks Sarek-Specific Configuration
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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.
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In addition to the global configuration described [here](../../sage.md), this Sarek-specific configuration includes the following tweaks:
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- 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:
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- Enable retries by default when exit codes relate to insufficient memory
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- Allow pending jobs to finish if the number of retries are exhausted
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- Slow the increase in the number of allocated CPU cores on retries
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- Define the `check_max()` function, which is missing in Sarek v2
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## Additional information about iGenomes
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@ -15,5 +15,4 @@ profiles {
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cfc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
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cfc_dev { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
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eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
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sage { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/sage.config" }
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}
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