Testing v0.1.1 (#20)

NAICNO · Sep 24, 2024 · 556ba52 · 556ba52
2 parents fff8335 + 92d014e
commit 556ba52
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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 .