F32 config and v9.2.0 (#112)

* Add F32 config

* Bump versions for release

CHANGELOG.md

@@ -8,6 +8,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [9.2.0] - 2022-11-18
+### Added
+- `F32.config` for resource allocation
 ### Changed
 - Use external resource allocation module
 - Parameterize Docker registry

config/F16.config

@@ -39,6 +39,10 @@ process {
         cpus = 2
         memory = 4.GB
     }
+    withName: deduplicate_records_SAMtools {
+        cpus = 2
+        memory = 4.GB
+    }
     withName: run_GetPileupSummaries_GATK {
         cpus = 1
         memory = 5.GB

config/F32.config

@@ -0,0 +1,94 @@
+process {
+    withName: run_validate_PipeVal {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_HaplotypeCallerVCF_GATK {
+        cpus = 2
+        memory = 4.GB
+    }
+    withName: run_HaplotypeCallerGVCF_GATK {
+        cpus = 2
+        memory = 4.GB
+    }
+    withName: run_MergeVcfs_Picard {
+        cpus = 1
+        memory = 15.GB
+    }
+    withName: run_RealignerTargetCreator_GATK {
+        cpus = 4
+        memory = 6.GB
+    }
+    withName: run_IndelRealigner_GATK {
+        cpus = 4
+        memory = 6.GB
+    }
+    withName: run_BaseRecalibrator_GATK {
+        cpus = 1
+        memory = 60.GB
+    }
+    withName: run_ApplyBQSR_GATK {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_index_SAMtools {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_MergeSamFiles_Picard {
+        cpus = 2
+        memory = 4.GB
+    }
+    withName: deduplicate_records_SAMtools {
+        cpus = 2
+        memory = 4.GB
+    }
+    withName: run_GetPileupSummaries_GATK {
+        cpus = 1
+        memory = 5.GB
+    }
+    withName: run_CalculateContamination_GATK {
+        cpus = 1
+        memory = 5.GB
+    }
+    withName: run_DepthOfCoverage_GATK {
+        cpus = 1
+        memory = 10.GB
+    }
+    withName: remove_intermediate_files {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: extract_GenomeIntervals {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_SplitIntervals_GATK {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_reheader_SAMtools {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: calculate_sha512 {
+        cpus = 1
+        memory = 1.GB
+    }
+    withName: run_VariantRecalibratorSNP_GATK {
+        cpus = 10
+        memory = 10.GB
+    }
+    withName: run_VariantRecalibratorINDEL_GATK {
+        cpus = 10
+        memory = 10.GB
+    }
+    withName: run_ApplyVQSR_GATK {
+        cpus = 10
+        memory = 10.GB
+    }
+    withName: filter_gSNP_GATK {
+        cpus = 10
+        memory = 10.GB
+    }
+}

nextflow.config

@@ -5,5 +5,5 @@ manifest {
     name = 'call-gSNP'
     author = ["Yash Patel", "Shu Tao", "Stefan Eng"]
     description = 'Nextflow pipeline to call germline short variants in single or normal-tumour paired mode'
-    version = '9.1.0'
+    version = '9.2.0'
 }