update clair3 params to be less strict

phac-nml · Nov 29, 2024 · 3c5566d · 3c5566d
1 parent d3c94eb
commit 3c5566d
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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"