Merge pull request #433 from ameynert/master

Updated documentation and DSL2 profile for Sarek

conf/eddie.config

@@ -46,5 +46,6 @@ singularity {
   runOptions = '-p -B "$TMPDIR"'
   enabled = true
   autoMounts = true
+  cacheDir = "/exports/igmm/eddie/BioinformaticsResources/nfcore/singularity-images"
 }
 

conf/pipeline/sarek/eddie.config

@@ -1,53 +1,77 @@
 process {
-
+  withName:APPLYBQSR {
-  withName:MapReads {
-    cpus = 16
-    memory = 128.GB
-    clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
-  }
-  withName:BuildDict {
-    cpus = 1
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:BamQC {
+  withName:APPLYBQSR_SPARK {
-    cpus = 8
-    memory = 128.GB
-    clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
-  }
-  withName:MarkDuplicates {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:BaseRecalibrator {
+  withName:GATK4_APPLYVQSR {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:ApplyBQSR {
+  withName:GATK4_BASERECALIBRATOR {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GatherBQSRReports {
+  withName:GATK4_BASERECALIBRATOR_SPARK {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:HaplotypeCaller {
+  withName:GATK4_CALCULATECONTAMINATION {  
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:GenotypeGVCFs {
+  withName:GATK4_CNNSCOREVARIANTS {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:Mutect2 {
+  withName:GATK4_CREATESEQUENCEDICTIONARY {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:MergeMutect2Stats {
+  withName:GATK4_ESTIMATELIBRARYCOMPLEXITY {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:PileupSummariesForMutect2 {
+  withName:GATK4_FILTERMUTECTCALLS {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:MergePileupSummaries {
+  withName:GATK4_FILTERVARIANTTRANCHES {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:CalculateContamination {  
+  withName:GATK4_GATHERBQSRREPORTS {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
-  withName:FilterMutect2Calls {
+  withName:GATK4_GATHERPILEUPSUMMARIES {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_GENOMICSDBIMPORT {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_GENOTYPEGVCFS {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_GETPILEUPSUMMARIES {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_HAPLOTYPECALLER {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_INTERVALLISTTOBED {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_LEARNREADORIENTATIONMODEL {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_MARKDUPLICATES {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_MARKDUPLICATES_SPARK {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_MERGEMUTECTSTATS {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_MERGEVCFS {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_MUTECT2 {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GATK4_VARIANTRECALIBRATOR {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
 }

docs/eddie.md

@@ -35,16 +35,17 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul
 
 ## Singularity set-up
 
-Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to the BioinformaticsResources path below. If some containers for your pipeline run are not present, please contact the [IGC Data Manager](data.manager@igc.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
+Load Singularity from the module system.
-
-If you do not have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
 
 ```bash
 module load singularity
-export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/BioinformaticsResources/nf-core/singularity-images"
 ```
 
-Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.
+The eddie profile is set to use `/exports/igmm/eddie/BioinformaticsResources/nfcore/singularity-images` as the Singularity cache directory. If some containers for your pipeline run are not present, please contact the [IGC Data Manager](data.manager@igc.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
+
+If you do not have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
+
+Singularity will by default create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.
 
 ```bash
 cd $HOME