Merge pull request #29 from Sydney-Informatics-Hub/glnexus-jemalloc

Change glnexus container
Sydney-Informatics-Hub · May 20, 2024 · 89dca30 · 89dca30
2 parents 5aeb10d + 2c41964
commit 89dca30
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Showing 2 changed files with 8 additions and 5 deletions.
diff --git a/config/gadi.config b/config/gadi.config
@@ -71,7 +71,7 @@ process {
 	withName: 'multiqc' {
 		queue = 'normalbw'
 		cpus = 1
-		memory = 4.Gb
+		memory = 10.Gb
 	}
 
 	withName: 'pb_fq2bam' {
@@ -99,7 +99,10 @@ process {
 	}
 
 	withName: 'glnexus_joint_call' {
-		executor = 'local'
+    queue = 'normal'
+    cpus = 48
+    time = '10h'
+    memory = 190.Gb
 	}
 
 	withName: 'download_vep' {
@@ -123,4 +126,4 @@ trace {
     overwrite = false
     file = "${params.outdir}/runInfo/gadi-nf-core-trace-${trace_timestamp}.txt"
     fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
-}
+}
diff --git a/modules/glnexus_joint.nf b/modules/glnexus_joint.nf
@@ -1,7 +1,7 @@
 process glnexus_joint_call {
     tag "JOINT GENOTYPING: ${params.cohort_name}" 
     publishDir "${params.outdir}/variants", mode: 'symlink'
-    container "quay.io/biocontainers/glnexus:1.4.1--h5c1b0a6_3"
+    container "ghcr.io/dnanexus-rnd/glnexus:v1.4.1"
 
     input:
     path(gvcf_list) 
@@ -26,4 +26,4 @@ process glnexus_joint_call {
       > ${params.cohort_name}.bcf \
       $args
     """
-}
+}