From cf4673201836656359e6f3a08f4ede691d3dfcbe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jo=C3=A3o=20Vitor?= <jvfecav@gmail.com>
Date: Thu, 22 Jun 2023 12:14:20 -0300
Subject: [PATCH] refactor: Increase default reqs for ppanggolin and
 create_report (#137)

* refactor: Increase default reqs for ppanggolin and create_report

* chore: Update test config
---
 conf/base.config                          | 4 ++--
 conf/test.config                          | 3 +++
 modules/local/chunked_fasttree.nf         | 2 +-
 modules/local/create_report.nf            | 3 ++-
 modules/local/ppanggolin/msa/main.nf      | 3 ++-
 modules/local/ppanggolin/workflow/main.nf | 3 ++-
 tests/nextflow.config                     | 3 +++
 7 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index 3be7b7d0..179fa78a 100755
--- a/conf/base.config
+++ b/conf/base.config
@@ -37,7 +37,7 @@ process {
         time   = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 12     * task.attempt, 'cpus'    ) }
+        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
         memory = { check_max( 48.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 8.h   * task.attempt, 'time'    ) }
     }
@@ -50,7 +50,7 @@ process {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 125.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 240.GB, 'memory' ) }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/conf/test.config b/conf/test.config
index ced5542f..2a114e53 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -53,4 +53,7 @@ process {
         memory = 6.GB
         time   = 4.h
     }
+    withLabel:process_high_memory {
+        memory = 6.GB
+    }
 }
diff --git a/modules/local/chunked_fasttree.nf b/modules/local/chunked_fasttree.nf
index 46578dff..7143bf4d 100644
--- a/modules/local/chunked_fasttree.nf
+++ b/modules/local/chunked_fasttree.nf
@@ -1,5 +1,5 @@
 process CHUNKED_FASTTREE {
-    label 'process_medium'
+    label 'process_high'
 
     conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/local/create_report.nf b/modules/local/create_report.nf
index afc12223..1f8c83ca 100644
--- a/modules/local/create_report.nf
+++ b/modules/local/create_report.nf
@@ -1,5 +1,6 @@
 process CREATE_REPORT {
-    label "process_medium"
+    label 'process_high'
+    label 'process_high_memory'
 
     conda (params.enable_conda ? "conda-forge::pandas=1.4.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/modules/local/ppanggolin/msa/main.nf b/modules/local/ppanggolin/msa/main.nf
index 83fc94fa..ecd8c0dd 100644
--- a/modules/local/ppanggolin/msa/main.nf
+++ b/modules/local/ppanggolin/msa/main.nf
@@ -1,6 +1,7 @@
 process PPANGGOLIN_MSA {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
+    label 'process_high_memory'
 
     conda "bioconda::ppanggolin=1.2.105"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/local/ppanggolin/workflow/main.nf b/modules/local/ppanggolin/workflow/main.nf
index d3b82527..2302529f 100644
--- a/modules/local/ppanggolin/workflow/main.nf
+++ b/modules/local/ppanggolin/workflow/main.nf
@@ -1,6 +1,7 @@
 process PPANGGOLIN_WORKFLOW {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
+    label 'process_high_memory'
 
     conda "bioconda::ppanggolin=1.2.105"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/tests/nextflow.config b/tests/nextflow.config
index a02cf5fa..7b166344 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -32,4 +32,7 @@ process {
         memory = 4.GB
         time   = 4.h
     }
+    withLabel:process_high_memory {
+        memory = 4.GB
+    }
 }