Add Sage-specific Sarek config

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)
@@ -203,6 +202,7 @@ 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)

conf/pipeline/sarek/sage.config

@@ -0,0 +1,37 @@
+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
+        }
+    }
+}

docs/pipeline/sarek/sage.md

@@ -0,0 +1,7 @@
+# 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.

docs/sage.md

@@ -1,12 +1,14 @@
-# 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
 
 ## Additional information about iGenomes
 

pipeline/sarek.config

@@ -15,4 +15,5 @@ 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" }
+}