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

Include `check_max()` definition for Sage configuration

README.md

@@ -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)

conf/sage.config

@@ -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
+        }
+    }
+}

docs/sage.md

@@ -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`
+This global configuration includes the following tweaks:
-- Increasing the default time limits because we run pipelines on AWS
+
-- Enabling retries by default when exit codes relate to insufficient memory
+- 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
 

pipeline/sarek.config

@@ -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" }
-}
+}