Add Tuebingen specific configuration parameters

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 
 -   [#671](https://github.com/SciLifeLab/Sarek/pull/671) - New `publishDirMode` param and docs
+-   [#673](https://github.com/SciLifeLab/Sarek/pull/673) - Profiles for BinAC and CFC clusters in Tübingen
 
 ### `Changed`
 

conf/binac.config

@@ -16,6 +16,7 @@ process {
 }
 
 params {
+  publishDirMode = 'symlink' 
   max_memory = 128.GB
   max_cpus = 28
   max_time = 48.h

conf/cfc.config

@@ -0,0 +1,22 @@
+/*
+ * -------------------------------------------------------------
+ *  Nextflow config file for use with Singularity on CFC at QBIC
+ * -------------------------------------------------------------
+ * Defines basic usage limits and singularity image id.
+ */
+
+/*
+*To be improved by process specific configuration asap, once our CFC cluster has the extra options removed - till then, task.attempt in NextFlow is not supported there.
+*/
+
+process {
+  beforeScript = 'module load qbic/singularity_slurm/2.5.2'
+  executor = 'slurm'
+}
+
+params {
+  publishDirMode = 'symlink' 
+  max_memory = 60.GB
+  max_cpus = 20
+  max_time = 140.h
+}

conf/resources.config

@@ -0,0 +1,104 @@
+/*
+ * -------------------------------------------------
+ * Nextflow config file for Sarek
+ * -------------------------------------------------
+ * Generalized resource configuration for clusters
+ * -------------------------------------------------
+ */
+
+params {
+  singleCPUMem  = 7.GB // for processes that are using more memory but a single CPU only. Use the 'core' queue for these
+}
+
+process {
+  cpus = { check_max( 10, 'cpus' ) }
+  memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+  time = { check_max( 8.h * task.attempt, 'time' ) }
+
+  errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'}
+  maxErrors = '-1'
+  maxRetries = 3
+
+  withName:MapReads {
+    memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+    cpus = { check_max( 10, 'cpus' ) }
+  } 
+  withName:CreateRecalibrationTable {
+    cpus = { check_max( 12, 'cpus' ) }
+    memory = {params.singleCPUMem * 8 * task.attempt}
+  }
+  withName:MarkDuplicates {
+		// Actually the -Xmx value should be kept lower
+    cpus = { check_max( 16, 'cpus' ) }
+    memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+  }
+  withName:MergeBams {
+    memory = {params.singleCPUMem * task.attempt}
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RecalibrateBam {
+    cpus = { check_max( 12, 'cpus' ) }
+    memory = { check_max( 7.GB * 8 * task.attempt, 'memory' ) }
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RunAlleleCount {
+    cpus = { check_max( 1, 'cpus' ) }
+    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
+  }
+  withName:RunAscat {
+    cpus = { check_max( 1, 'cpus' ) }
+    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
+  }
+  withName:RunBcftoolsStats {
+    cpus = { check_max( 1, 'cpus' ) }
+  }
+  withName:RunConvertAlleleCounts {
+    cpus = { check_max( 1, 'cpus' ) }
+    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
+  }
+  withName:RunFastQC {
+    cpus = { check_max( 2, 'cpus' ) } // FastQC is only capable of running one thread per fastq file.
+    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+  }
+  withName:RunFreeBayes {
+    cpus = { check_max( 1, 'cpus' ) }
+    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+  }
+  withName:RunHaplotypecaller {
+    cpus = { check_max( 20, 'cpus' ) }
+    // Increase memory quadratically
+    memory = { check_max( 7.GB * 2 * task.attempt, 'memory' ) }
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RunGenotypeGVCFs {
+    cpus = { check_max( 20, 'cpus' ) }
+    memory = { check_max( 7.GB * task.attempt, 'memory' ) }
+  }
+  withName:RunMultiQC {
+    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+  }
+  withName:RunMutect2 {
+    cpus = { check_max( 2, 'cpus' ) }
+    memory = { check_max( 7.GB * task.attempt, 'memory' ) }
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RunSamtoolsStats {
+    cpus = { check_max( 2, 'cpus' ) }
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RunSingleStrelka {
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RunSnpeff {
+    cpus = { check_max( 1, 'cpus' ) }
+    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+  }
+  withName:RunStrelka {
+    cpus = { check_max( 1, 'cpus' ) }
+    time = { check_max( 5.h * task.attempt, 'time' ) }
+  }
+  withName:RunVEP {
+    cpus = { check_max( 1, 'cpus' ) }
+    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+  }
+}

nextflow.config

@@ -87,6 +87,16 @@ profiles {
     includeConfig 'conf/base.config'
     includeConfig 'conf/binac.config'
     includeConfig 'conf/singularity.config'
+    includeConfig 'conf/resources.config'
     includeConfig 'conf/containers.config'
   }
+  // Default config for CFC cluster in Tuebingen/Germany 
+  cfc {
+    includeConfig 'conf/base.config'
+    includeConfig 'conf/cfc.config'
+    includeConfig 'conf/singularity.config'
+    includeConfig 'conf/resources.config'
+    includeConfig 'conf/containers.config'
+  }
+
 }