Ensure checkmax is still used

nf-core · Oct 3, 2024 · ce449f2 · ce449f2
1 parent 9d7ce62
commit ce449f2
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -120,22 +120,22 @@ process {
     }
     //MEGAHIT returns exit code 250 when running out of memory
     withName: MEGAHIT {
-        cpus          = { params.megahit_fix_cpu_1 ? 1 : 8 * task.attempt }
+        cpus          = { params.megahit_fix_cpu_1 ? 1 : check_max(8 * task.attempt, 'cpus') }
         memory        = { check_max(40.GB * task.attempt, 'memory') }
         time          = { check_max(16.h * task.attempt, 'time') }
         errorStrategy = { task.exitStatus in ((130..145) + 104 + 250) ? 'retry' : 'finish' }
     }
     //SPAdes returns error(1) if it runs out of memory (and for other reasons as well...)!
     //exponential increase of memory and time with attempts, keep number of threads to enable reproducibility
     withName: METASPADES {
-        cpus          = { params.spades_fix_cpus != -1 ? params.spades_fix_cpus : 10 * task.attempt }
+        cpus          = { params.spades_fix_cpus != -1 ? params.spades_fix_cpus : check_max(10 * task.attempt, 'cpus') }
         memory        = { check_max(64.GB * (2 ** (task.attempt - 1)), 'memory') }
         time          = { check_max(24.h * (2 ** (task.attempt - 1)), 'time') }
         errorStrategy = { task.exitStatus in ((130..145) + 104 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     withName: METASPADESHYBRID {
-        cpus          = { params.spadeshybrid_fix_cpus != -1 ? params.spadeshybrid_fix_cpus : 10 * task.attempt }
+        cpus          = { params.spadeshybrid_fix_cpus != -1 ? params.spadeshybrid_fix_cpus : check_max(10 * task.attempt, 'cpus') }
         memory        = { check_max(64.GB * (2 ** (task.attempt - 1)), 'memory') }
         time          = { check_max(24.h * (2 ** (task.attempt - 1)), 'time') }
         errorStrategy = { task.exitStatus in [143, 137, 21, 1] ? 'retry' : 'finish' }