update dependency

bactopia · Apr 6, 2023 · bc7322e · bc7322e
1 parent 9d01454
commit bc7322e
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Showing 2 changed files with 13 additions and 37 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -16,56 +16,32 @@ process {
         }
     ]
 
-    // single cpus
-    withLabel: max_cpus_1 {
-        cpus = {check_max('request', RESOURCES.MAX_CPUS_1, 'cpus')}
-    }
-
-    // 75% cpus
-    withLabel: max_cpu_75 {
-        cpus = {check_max('request', RESOURCES.MAX_CPUS_75, 'cpus' )}
-    }
-
-    // Half cpus
-    withLabel: max_cpu_50 {
-        cpus = {check_max('request', RESOURCES.MAX_CPUS_50, 'cpus' )}
-    }
-
-    // Memory defaults
-    withLabel: base_mem_4gb {
-        memory = {check_max(4.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )}
-    }
-
-    withLabel: base_mem_8gb {
-        memory = {check_max(8.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )}
-    }
-
     // Process specific
     withLabel: 'assemble_genome' {
         memory = { meta.runtype == 'hybrid' || params.use_unicycler ? check_max((32.GB * task.attempt), RESOURCES.MAX_MEMORY, 'memory') : check_max((8.GB * task.attempt), RESOURCES.MAX_MEMORY, 'memory')}
-        time = { meta.runtype == 'hybrid' ||  params.use_unicycler ? check_max( 2.h * task.attempt, (params.max_time).m, 'time' ) : check_max( (params.min_time).m * task.attempt, (params.max_time).m, 'time' )}
-    }
-
-    withLabel: 'gather_samples' {
-        maxForks = params.max_downloads
-        maxRetries = 20
+        time   = { meta.runtype == 'hybrid' || params.use_unicycler ? check_max( 2.h * task.attempt, (params.max_time).m, 'time' ) : check_max( (params.min_time).m * task.attempt, (params.max_time).m, 'time' )}
     }
 
     // Modules imported from nf-core
+    withLabel:process_single {
+        cpus   = { check_max('request'          , RESOURCES.MAX_CPUS  , 'cpus'   )}
+        memory = { check_max(4.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )}
+        time   = { check_max( 1.h * task.attempt, 2.h * task.attempt  , 'time'   )}
+    }
     withLabel: process_low {
-        cpus = {check_max('request', RESOURCES.MAX_CPUS, 'cpus')}
+        cpus   = {check_max('request'          , RESOURCES.MAX_CPUS  , 'cpus'   )}
         memory = {check_max(8.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )}
-        time = {check_max( 2.h * task.attempt, 2.h * task.attempt, 'time' )}
+        time   = {check_max( 2.h * task.attempt, 2.h * task.attempt  , 'time'   )}
     }
     withLabel: process_medium {
-        cpus = {check_max('request', RESOURCES.MAX_CPUS, 'cpus')}
+        cpus   = {check_max('request'           , RESOURCES.MAX_CPUS  , 'cpus'   )}
         memory = {check_max(16.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )}
-        time = {check_max( 12.h * task.attempt, 12.h * task.attempt, 'time' )}
+        time   = {check_max( 12.h * task.attempt, 12.h * task.attempt , 'time'   )}
     }
     withLabel: process_high {
-        cpus = {check_max('request', RESOURCES.MAX_CPUS, 'cpus')}
+        cpus   = {check_max('request'           , RESOURCES.MAX_CPUS  , 'cpus'   )}
         memory = {check_max(64.GB * task.attempt, RESOURCES.MAX_MEMORY, 'memory' )}
-        time = {check_max( 24.h * task.attempt, 24.h * task.attempt, 'time' )}
+        time   = {check_max( 24.h * task.attempt, 24.h * task.attempt , 'time'   )}
     }
     withLabel: process_long {
         time = {check_max( 96.h * task.attempt, 96.h * task.attempt, 'time' )}

diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml
@@ -16,7 +16,7 @@ requirements:
     - pip
     - python >3.8
   run:
-    - bactopia-py >=1.0.0
+    - bactopia-py >=1.0.1
     - conda >=22.11.0
     - coreutils
     - mamba >=1.1.0