More explicit cpu-hour handling

Author: viklund

main.nf

@@ -48,10 +48,9 @@ if (!bamindex) {
         module 'bioinfo-tools'
         module "$params.modules.samtools"
 
-        // We only need one core for this part
         executor choose_executor()
         queue 'core'
-        time params.short_job
+        time params.runtime.simple
 
         when: 'indexbam' in workflowSteps
 
@@ -79,7 +78,7 @@ process manta {
     module "$params.modules.manta"
 
     errorStrategy { task.exitStatus == 143 ? 'retry' : 'terminate' }
-    time { params.long_job * 2**(task.attempt-1) }
+    time { params.runtime.caller * 2**(task.attempt-1) }
     maxRetries 3
     queue 'core'
     cpus 4
@@ -116,10 +115,9 @@ if (!params.fastq) {
         module 'bioinfo-tools'
         module "$params.modules.samtools"
 
-        // We only need one core for this part
         executor choose_executor()
         queue 'core'
-        time params.short_job
+        time params.runtime.simple
 
         when: 'fastq' in workflowSteps
 
@@ -142,6 +140,11 @@ process fermikit {
 
     publishDir params.outdir, mode: 'copy'
 
+    errorStrategy { task.exitStatus == 143 ? 'retry' : 'terminate' }
+    time { params.runtime.fermikit * 2**( task.attempt - 1 ) }
+    maxRetries 3
+    queue 'node'
+
     module 'bioinfo-tools'
     module "$params.modules.fermikit"
     module "$params.modules.samtools"
@@ -184,10 +187,9 @@ process mask_beds {
 
     publishDir params.outdir, mode: 'copy'
 
-    // Does not use many resources, run it locally
     executor choose_executor()
     queue 'core'
-    time params.short_job
+    time params.runtime.simple
 
     module 'bioinfo-tools'
     module "$params.modules.bedtools"
@@ -220,10 +222,9 @@ process intersect_files {
 
     publishDir params.outdir, mode: 'copy'
 
-    // Does not use many resources, run it locally
     executor choose_executor()
     queue 'core'
-    time params.short_job
+    time params.runtime.simple
 
     module 'bioinfo-tools'
     module "$params.modules.bedtools"
@@ -261,7 +262,7 @@ process variant_effect_predictor {
 
     executor choose_executor()
     queue 'core'
-    time params.short_job
+    time params.runtime.simple
 
     module 'bioinfo-tools'
     module "$params.modules.vep"
@@ -322,10 +323,9 @@ process snpEff {
     module 'bioinfo-tools'
     module "$params.modules.snpeff"
 
-    // Does not use many resources, run it locally
     executor choose_executor()
     queue 'core'
-    time params.short_job
+    time params.runtime.simple
 
     when: 'snpeff' in workflowSteps
 
@@ -371,8 +371,6 @@ def usage_message() {
     log.info '    --steps         Specify what steps to run, comma separated:'
     log.info '                Callers: manta, fermikit, cnvnator (choose one or many)'
     log.info '                Annotation: vep OR snpeff'
-    log.info '    --long_job      Running time for long job (callers, fermi and manta)'
-    log.info '    --short_job     Running time for short jobs (bam indexing and bam2fq)'
     log.info '    --outdir        Directory where resultfiles are stored'
     log.info ''
 }
@@ -439,6 +437,8 @@ def nextflow_running_as_slurmjob() {
     return false
 }
 
+/* If the nextflow deamon is running as a slurm job, we can use the local CPU
+ * for a lot of our work */
 def choose_executor() {
     return nextflow_running_as_slurmjob() ? 'local' : 'slurm'
 }

nextflow.config

@@ -25,14 +25,15 @@ params {
         assembly = "GRCh37"
     }
 
-    long_job  = '10h' // used for the callers (fermikit & manta)
-    short_job = '30m' // used for bam indexing and bam2fq
+    runtime {
+        simple = '30m'    // Short simple shell jobs
+        fermikit = '24h' // Fermikit is the longest running of them all
+        caller = '10h'  // The rest are a lot quicker
+    }
 }
 
 process {
   executor = 'slurm'
-  time = params.long_job
-  queue = "node"
   clusterOptions = {
       "-A $params.project"
   }