removed redundant vadr memory variable

jinfinance · Jun 14, 2021 · f97efc5 · f97efc5
1 parent 8dd82bf
commit f97efc5
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Showing 2 changed files with 4 additions and 9 deletions.
diff --git a/Cecret.nf b/Cecret.nf
@@ -416,7 +416,7 @@ process sort {
     date | tee -a $log_file $err_file > /dev/null
     samtools --version >> $log_file
 
-    samtools sort -@ !{task.cpus} !{sam} 2>> $err_file | \
+    samtools sort !{sam} 2>> $err_file | \
       samtools view -F 4 -o aligned/!{sample}.sorted.bam 2>> $err_file >> $log_file
 
     # indexing the bams
@@ -577,10 +577,6 @@ process ivar_variants {
   errorStrategy {'retry'}
   maxRetries 2
 
-  memory {2.GB * task.attempt}
-  errorStrategy {'retry'}
-  maxRetries 2
-
   when:
   params.ivar_variants
 
@@ -1247,8 +1243,7 @@ nextclade_files
     sort: true,
     storeDir: "${params.outdir}/nextclade")
 
-params.maxmem = Math.round(Runtime.runtime.totalMemory() / 10241024)
-if ( params.maxmem / 2 > params.medcpus && params.vadr ) {
+if ( Math.round(Runtime.runtime.totalMemory() / 10241024) / 2 > params.medcpus && params.vadr ) {
   vadrmemory = params.medcpus + params.medcpus
   vadrcpus = params.medcpus
 } else {

diff --git a/Cecret_annotation.nf b/Cecret_annotation.nf
@@ -132,14 +132,14 @@ process nextclade {
 }
 
 params.vadr = true
-params.maxmem = Math.round(Runtime.runtime.totalMemory() / 10241024)
-if ( params.maxmem / 2 > params.medcpus ) {
+if ( Math.round(Runtime.runtime.totalMemory() / 10241024) / 2 > params.medcpus && params.vadr ) {
   vadrmemory = params.medcpus + params.medcpus
   vadrcpus = params.medcpus
 } else {
   vadrmemory = 2
   vadrcpus = 1
 }
+
 params.vadr_options = '--split --glsearch -s  -r --nomisc --lowsim5term 2 --lowsim3term 2 --alt_fail lowscore,fstukcnf,insertnn,deletinn'
 params.vadr_reference = 'sarscov2'
 params.vadr_mdir = '/opt/vadr/vadr-models'