Remove local set_env and check_limits methods

CHANGELOG.md

@@ -14,8 +14,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Add new flow diagram to README
 - Add additional details to Pipeline Steps section of README
 - Option to provide base recalibration tables for any subset of samples to skip `BaseRecalibrator`
+
 ### [Changed]
 - Use modularized `set_env` function
+- Use modularized `check_limits` function
 
 ---
 

config/methods.config

@@ -6,42 +6,6 @@ includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/schema/sch
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/retry/retry.config"
 
 methods {
-    // Function to ensure that resource requirements don't go beyond
-    // a maximum limit or below a minimum limit
-    check_limits = { 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 if (obj.compareTo(params.min_memory as nextflow.util.MemoryUnit) == -1)
-                    return params.min_memory as nextflow.util.MemoryUnit
-                else
-                    return obj
-            } catch (all) {
-                println "   ### WARNING ###   Max memory '${params.max_memory}' or min memory '${params.min_memory}' is not valid! Using default value: $obj"
-                return obj
-            }
-        } else if (type == 'time') {
-            try {
-                if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                    return params.max_time as nextflow.util.Duration
-                else if (obj.compareTo(params.min_time as nextflow.util.Duration) == -1)
-                    return params.min_time as nextflow.util.Duration
-                else
-                    return obj
-            } catch (all) {
-                println "   ### WARNING ###   Max time '${params.max_time}' or min time '${params.min_time}' is not valid! Using default value: $obj"
-                return obj
-            }
-        } else if (type == 'cpus') {
-            try {
-                return Math.max( Math.min( obj, params.max_cpus as int ), params.min_cpus as int )
-            } catch (all) {
-                println "   ### WARNING ###   Max cpus '${params.max_cpus}' or min cpus '${params.min_cpus}' is not valid! Using default value: $obj"
-                return obj
-            }
-        }
-    }
 
     set_log_output_dir = {
         def tz = TimeZone.getTimeZone("UTC")