From 3c5566d6bdd593b4190c57357ea16ad8d5ac48e7 Mon Sep 17 00:00:00 2001
From: Darian Hole <darian.hole@canada.ca>
Date: Fri, 29 Nov 2024 15:08:05 -0600
Subject: [PATCH] update clair3 params to be less strict

---
 conf/base.config                        | 8 +++++---
 modules/local/nanopore_amplicon/main.nf | 3 +--
 modules/local/nanopore_shotgun/main.nf  | 3 +--
 modules/local/visualization/main.nf     | 2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index a7aef84..967fa13 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -26,12 +26,12 @@ process {
     withLabel: process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        time   = { check_max( 6.h  * task.attempt, 'time'    ) }
     }
     withLabel: process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 8.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        time   = { check_max( 6.h   * task.attempt, 'time'    ) }
     }
     withLabel: process_medium {
         cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
@@ -47,7 +47,9 @@ process {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
     withLabel: process_high_memory {
-        memory = { check_max( 90.GB * task.attempt, 'memory' ) }
+        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 32.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h  * task.attempt, 'time'    ) }
     }
     withLabel: error_ignore {
         errorStrategy = 'ignore'
diff --git a/modules/local/nanopore_amplicon/main.nf b/modules/local/nanopore_amplicon/main.nf
index 63e75b3..756cd8d 100644
--- a/modules/local/nanopore_amplicon/main.nf
+++ b/modules/local/nanopore_amplicon/main.nf
@@ -174,8 +174,7 @@ process CLAIR3_VARIANTS {
         --platform='ont' \\
         --model_path="\$MODEL_PATH" \\
         --output="${sampleName}-out" \\
-        --qual=3 \\
-        --min_coverage=20 \\
+        --min_coverage=10 \\
         --haploid_precise \\
         --enable_long_indel \\
         --fast_mode \\
diff --git a/modules/local/nanopore_shotgun/main.nf b/modules/local/nanopore_shotgun/main.nf
index d5262fd..977589c 100644
--- a/modules/local/nanopore_shotgun/main.nf
+++ b/modules/local/nanopore_shotgun/main.nf
@@ -171,8 +171,7 @@ process CLAIR3_VARIANTS {
         --platform='ont' \\
         --model_path="\$MODEL_PATH" \\
         --output="${sampleName}-out" \\
-        --qual=2 \\
-        --min_coverage=20 \\
+        --min_coverage=10 \\
         --haploid_precise \\
         --enable_long_indel \\
         --fast_mode \\
diff --git a/modules/local/visualization/main.nf b/modules/local/visualization/main.nf
index 5fceb84..8a37e24 100644
--- a/modules/local/visualization/main.nf
+++ b/modules/local/visualization/main.nf
@@ -1,7 +1,7 @@
 // Visualization Modules
 //  Custom scripts are versioned here
 process CREATE_READ_VARIATION_CSV {
-    label 'process_single'
+    label 'process_high_memory'
     tag "$meta.id"
     publishDir "${params.outdir}/variation_csvs", pattern: "*.csv", mode: "copy"