From fa4075c2a0302995efdb0558ddafcbbe0b82ecfa Mon Sep 17 00:00:00 2001
From: "Thiseas C. Lamnidis" <thisseass@gmail.com>
Date: Thu, 10 Feb 2022 10:00:18 +0100
Subject: [PATCH] Removed all time limits

---
 conf/pipeline/eager/eva.config | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index d436895..67c3b5a 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -19,43 +19,36 @@ process {
   withLabel:'sc_tiny'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 1.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
   }
 
   withLabel:'sc_small'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 4.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
   }
 
   withLabel:'sc_medium'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
   }
 
   withLabel:'mc_small'{
     cpus = { check_max( 2, 'cpus' ) }
     memory = { check_max( 4.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
   }
 
   withLabel:'mc_medium' {
     cpus = { check_max( 4, 'cpus' ) }
     memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
   }
 
   withLabel:'mc_large'{
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-     time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
   }
 
   withLabel:'mc_huge'{
      cpus = { check_max( 32, 'cpus' ) }
      memory = { check_max( 256.GB * task.attempt, 'memory' ) }
-     time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
    }
   
   // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
@@ -196,43 +189,36 @@ profiles {
         withLabel:'sc_tiny'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_small'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_medium'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 12.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_small'{
           cpus = { check_max( 2, 'cpus' ) }
           memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_medium' {
           cpus = { check_max( 4, 'cpus' ) }
           memory = { check_max( 12.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_large'{
           cpus = { check_max( 8, 'cpus' ) }
           memory = { check_max( 24.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_huge'{
           cpus = { check_max( 32, 'cpus' ) }
           memory = { check_max( 256.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         // Fixes for SGE and Java incompatibility due to  (and also some samtools?!) using more memory than you tell it to use
@@ -297,7 +283,6 @@ profiles {
 
         withName:hostremoval_input_fastq {
           memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-          time = 1440.h
         }
 
         withName: maltextract {
@@ -378,43 +363,36 @@ profiles {
         withLabel:'sc_tiny'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 2.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_small'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_medium'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_small'{
           cpus = { check_max( 2, 'cpus' ) }
           memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_medium' {
           cpus = { check_max( 4, 'cpus' ) }
           memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_large'{
            cpus = { check_max( 8, 'cpus' ) }
            memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-           time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_huge'{
            cpus = { check_max( 32, 'cpus' ) }
            memory = { check_max( 512.GB * task.attempt, 'memory' ) }
-           time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
          }
 
         // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
@@ -469,7 +447,6 @@ profiles {
 
         withName:hostremoval_input_fastq {
           memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-          time = 1440.h
         }
 
         withName: metagenomic_complexity_filter {