From 92d014ed62bf30cb20639c890ed04cffce5a09db Mon Sep 17 00:00:00 2001
From: pubudu <p.s.samarakoon@usit.uio.no>
Date: Tue, 24 Sep 2024 14:00:16 +0200
Subject: [PATCH] update conf files

---
 workflows/conf/resource.conf        | 16 ++++++++--------
 workflows/nextflow.config           |  1 +
 workflows/templates/pbrun_fq2bam.sh |  1 +
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/workflows/conf/resource.conf b/workflows/conf/resource.conf
index 3c3e499..9f27f0a 100644
--- a/workflows/conf/resource.conf
+++ b/workflows/conf/resource.conf
@@ -34,24 +34,24 @@ process {
     // Specify resources for each process
 
     withName:'pbrun_fq2bam' {
-        memory='120 GB'
-        cpus='42'
+        memory='412 GB'
+        cpus='96'
         gpu='4'
     }
     // pbrun_applybqsr is recommended to run on 1 GPU
     withName:'pbrun_applybqsr' {
-        memory='120 GB'
-        cpus='42'
+        memory='412 GB'
+        cpus='96'
         gpu='1'
     }
     withName:'pbrun_deepvariant' {
-        memory='120 GB'
-        cpus='42'
+        memory='412 GB'
+        cpus='96'
         gpu='4'
     }
     withName:'pbrun_haplotypecaller' {
-        memory='120 GB'
-        cpus='42'
+        memory='412 GB'
+        cpus='96'
         gpu='4'
     }
     
diff --git a/workflows/nextflow.config b/workflows/nextflow.config
index f956bf0..3b9567a 100644
--- a/workflows/nextflow.config
+++ b/workflows/nextflow.config
@@ -38,6 +38,7 @@ profiles {
         apptainer.enabled = true
         apptainer.autoMounts = true
         includeConfig 'conf/slurm.conf'
+        includeConfig 'conf/resource.conf'
     }
     docker {
         docker.enabled = true
diff --git a/workflows/templates/pbrun_fq2bam.sh b/workflows/templates/pbrun_fq2bam.sh
index cbdfa9e..096b89f 100644
--- a/workflows/templates/pbrun_fq2bam.sh
+++ b/workflows/templates/pbrun_fq2bam.sh
@@ -16,6 +16,7 @@ pbrun fq2bam \
 --in-fq ${R1} ${R2}  \
 \${INTERVALS} \
 --knownSites \${KNOWN_SITES} \
+--num-gpus ${task.gpu} \
 --out-bam ${S_NAME}_pbrun_fq2bam_${PROCESSOR}.bam \
 --out-recal-file ${S_NAME}_${PROCESSOR}_recal_gpu.txt \
 --tmp-dir .
\ No newline at end of file