Complete check_max() move to global config

README.md

@@ -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)

conf/pipeline/sarek/sage.config

@@ -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
-        }
-    }
-}

conf/sage.config

@@ -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 {

docs/pipeline/sarek/sage.md

@@ -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.

docs/sage.md

@@ -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
 

pipeline/sarek.config

@@ -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" }
 }