Memory bumped & snpeff annotation file name updated to '*annotated.ra…

…w*' (#150) * Memory bumped & snpeff annotation file name updated to '*annotated.raw*' * export lines are updated Co-authored-by: TOLGA <ayazsevent@email.chop.edu>
chopdgd · Apr 21, 2020 · 674ae5d · 674ae5d
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Showing 58 changed files with 101 additions and 96 deletions.
diff --git a/arriba/arriba.wdl b/arriba/arriba.wdl
@@ -18,7 +18,7 @@ task Arriba {
     String userString = "-T -P"
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 2
 
     String fusion_output = "~{sample_id}" + '.arriba.fusions.tsv'

diff --git a/bcftools/Merge.wdl b/bcftools/Merge.wdl
@@ -21,7 +21,7 @@ task BCFToolsMerge {
 
     # Run time variables
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     # Output file names

diff --git a/bedtools/BamToFastQ.wdl b/bedtools/BamToFastQ.wdl
@@ -17,7 +17,7 @@ task BamToFastQ {
     String ? fastq2
 
     Array[String] modules = []
-    Float memory = 1
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/bedtools/Intersect.wdl b/bedtools/Intersect.wdl
@@ -17,7 +17,7 @@ task Intersect {
     String userString = "-wao"
 
     Array[String] modules = []
-    Float memory = 1
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = basename(bed_a, ".bed") + '.intersect.bed'

diff --git a/bedtools/Merge.wdl b/bedtools/Merge.wdl
@@ -18,7 +18,7 @@ task Merge {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 1
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = basename(bed, ".bed") + '.merged.bed'

diff --git a/freebayes/FreeBayes.wdl b/freebayes/FreeBayes.wdl
@@ -23,7 +23,7 @@ task FreeBayes {
     String userString = "-4 -q 15 -F 0.03"
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = sample_id + '.freebayes.vcf'

diff --git a/gatk/CombineVariants.wdl b/gatk/CombineVariants.wdl
@@ -27,7 +27,7 @@ task CombineVariants {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = filename_prefix + ".merged.vcf.gz"

diff --git a/gatk/GenotypeGVCFs.wdl b/gatk/GenotypeGVCFs.wdl
@@ -28,7 +28,7 @@ task GenotypeGVCFs {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 1
 
     String vcf_filename = cohort_id + ".rawVariants.vcf.gz"

diff --git a/gatk/HaplotypeCallerERC.wdl b/gatk/HaplotypeCallerERC.wdl
@@ -30,7 +30,7 @@ task HaplotypeCallerERC {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 1
 
     String gvcf_filename = sample_id + ".rawLikelihoods.g.vcf.gz"

diff --git a/gatk/SelectVariants.wdl b/gatk/SelectVariants.wdl
@@ -26,7 +26,7 @@ task SelectVariants {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 6
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = basename(input_file) + ".filtered.vcf.gz"

diff --git a/gatk/VariantFiltration.wdl b/gatk/VariantFiltration.wdl
@@ -25,7 +25,7 @@ task VariantFiltration {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 6
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = basename(input_file) + ".filtered.vcf.gz"

diff --git a/git/commands.wdl b/git/commands.wdl
@@ -13,7 +13,7 @@ task Clone {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 1
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/kallisto/kallisto.wdl b/kallisto/kallisto.wdl
@@ -17,7 +17,7 @@ task Kallisto {
     String userString = "-b 10"
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 4
   }
 

diff --git a/mitolib/haplochecker.wdl b/mitolib/haplochecker.wdl
@@ -18,7 +18,7 @@ task ContaminationCheck {
     String userString = "--VAF 0.015 --QUAL 20 --MAPQ 20"
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = sample_name + "/" + sample_name + ".sorted.contamination.txt"

diff --git a/mitolib/haplogrep.wdl b/mitolib/haplogrep.wdl
@@ -17,7 +17,7 @@ task HaploGrep {
     String ? userString
 
     # Run time variables
-    Float memory = 6
+    Float memory = 12
     Int cpu = 1
     Array[String] modules = []
 

diff --git a/mutect/MuTect.wdl b/mutect/MuTect.wdl
@@ -27,7 +27,7 @@ task MuTect {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String vcf_filename = sample_id + "_MuTect.vcf"

diff --git a/penncnv/DetectCNVs.wdl b/penncnv/DetectCNVs.wdl
@@ -17,7 +17,7 @@ task DetectCNVs {
     String ? sex_flag = ""  # NOTE: PennCNV needs -chrX flag to call on Sex Chr
 
     # Run time variables
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
     Array[String] modules = []
 

diff --git a/penncnv/MergeCNV.wdl b/penncnv/MergeCNV.wdl
@@ -13,7 +13,7 @@ task MergeCNV {
     File signal_file
 
     # Run time variables
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
     Array[String] modules = []
 

diff --git a/penncnv/ScanRegion.wdl b/penncnv/ScanRegion.wdl
@@ -13,7 +13,7 @@ task ScanRegion {
     File refgene_file
 
     # Run time variables
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
     Array[String] modules = []
   }

diff --git a/penncnv/VisualizeCNV.wdl b/penncnv/VisualizeCNV.wdl
@@ -13,7 +13,7 @@ task VisualizeCNV {
     File idmap_file
 
     # Run time variables
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
     Array[String] modules = []
 

diff --git a/picard/AddOrReplaceReadGroups.wdl b/picard/AddOrReplaceReadGroups.wdl
@@ -25,7 +25,7 @@ task AddOrReplaceReadGroups {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = "~{sample_id}" + "~{output_filename_extension}"

diff --git a/picard/BedToIntervalList.wdl b/picard/BedToIntervalList.wdl
@@ -20,7 +20,7 @@ task BedToIntervalList {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 16
     Int cpu = 1
     String output_filename = basename(bed_file) + ".interval_list"
   }

diff --git a/picard/CollectHsMetrics.wdl b/picard/CollectHsMetrics.wdl
@@ -24,7 +24,7 @@ task CollectHsMetrics {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 16
     Int cpu = 1
 
     String per_target_coverage_filename = sample_id + ".HsMetrics.target"

diff --git a/picard/MarkDuplicates.wdl b/picard/MarkDuplicates.wdl
@@ -23,7 +23,7 @@ task MarkDuplicates {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 16
     Int cpu = 1
 
     String metrics_filename = sample_id + ".picardmkdup.metrics"

diff --git a/pindel/Pindel.wdl b/pindel/Pindel.wdl
@@ -24,7 +24,7 @@ task Pindel {
     String userString = "-t"
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/pindel/Pindel2VCF.wdl b/pindel/Pindel2VCF.wdl
@@ -21,7 +21,7 @@ task Pindel2Vcf {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 12
     Int cpu = 1
 
     String temp_filename = basename(input_file) + '_merged_pindel_files'

diff --git a/pizzly/pizzly-flatten-json.wdl b/pizzly/pizzly-flatten-json.wdl
@@ -16,7 +16,7 @@ task PizzlyFlattenJSON {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 1
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = "~{sample_id}" + '.genetable.txt'

diff --git a/pizzly/pizzly.wdl b/pizzly/pizzly.wdl
@@ -20,7 +20,7 @@ task Pizzly {
     Int insert_size = 400
 
     Array[String] modules = []
-    Float memory = 1
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/python/virtualenv.wdl b/python/virtualenv.wdl
@@ -11,7 +11,7 @@ task CreateVirtualenv {
     Array[String] python_modules = ['python/2.7']
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 16
     Int cpu = 1
 
     String python_binary = name + "/bin/python"

diff --git a/rnaseqc/rnaseqc.wdl b/rnaseqc/rnaseqc.wdl
@@ -18,7 +18,7 @@ task RNASeQC {
     String userString = "--coverage"
 
     Array[String] modules = []
-    Float memory = 2
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/samtools/ExtractMappedReads.wdl b/samtools/ExtractMappedReads.wdl
@@ -18,7 +18,7 @@ task ExtractMappedReads {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = basename(input_file) + ".mapped.bam"

diff --git a/samtools/Index.wdl b/samtools/Index.wdl
@@ -15,7 +15,7 @@ task Index {
     String output_file
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/samtools/MPileup.wdl b/samtools/MPileup.wdl
@@ -18,7 +18,7 @@ task MPileup {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/samtools/Samtools.wdl b/samtools/Samtools.wdl
@@ -16,7 +16,7 @@ task Samtools {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
   }
 

diff --git a/scalpel/Single.wdl b/scalpel/Single.wdl
@@ -25,7 +25,7 @@ task Single {
     String userString = "--mapscore 15 --intarget --format vcf"
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = sample_id + "/variants.indel.vcf"

diff --git a/slivar/compound-hets.wdl b/slivar/compound-hets.wdl
@@ -18,7 +18,7 @@ task compoundHets {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = prefix + '.slivar.comphets.vcf'

diff --git a/slivar/expr.wdl b/slivar/expr.wdl
@@ -23,7 +23,7 @@ task expr {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = prefix + '.slivar.expr.vcf'

diff --git a/slivar/make-gnotate.wdl b/slivar/make-gnotate.wdl
@@ -17,7 +17,7 @@ task makeGnotate {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 4
+    Float memory = 12
     Int cpu = 1
 
     String output_filename = prefix + '.zip'

diff --git a/snpeff/SnpEff.wdl b/snpeff/SnpEff.wdl
@@ -22,7 +22,7 @@ task SnpEff {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 8
+    Float memory = 16
     Int cpu = 1
 
     String output_filename = filename_prefix + '.snpeff.vcf'

diff --git a/snpeff/SnpSift.wdl b/snpeff/SnpSift.wdl
@@ -26,7 +26,7 @@ task SnpSift {
     String ? userString
 
     Array[String] modules = []
-    Float memory = 12
+    Float memory = 16
     Int cpu = 1
 
     String output_filename = filename_prefix + '.snpsift.vcf'

diff --git a/subworkflows/BAM-Quality-Control.wdl b/subworkflows/BAM-Quality-Control.wdl
@@ -8,9 +8,9 @@ version 1.0
 # -------------------------------------------------------------------------------------------------
 
 
-import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.0/gatk/DepthOfCoverage.wdl" as DepthOfCoverage
-import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.0/picard/CollectHsMetrics.wdl" as CollectHsMetrics
-import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.0/verifybamid/VerifyBamId.wdl" as VerifyBamId
+import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.1/gatk/DepthOfCoverage.wdl" as DepthOfCoverage
+import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.1/picard/CollectHsMetrics.wdl" as CollectHsMetrics
+import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.1/verifybamid/VerifyBamId.wdl" as VerifyBamId
 
 workflow BAMQualityControl {
   input {

diff --git a/subworkflows/Mito-SnpEff-Annotation.wdl b/subworkflows/Mito-SnpEff-Annotation.wdl
@@ -6,9 +6,9 @@ version 1.0
 #  * SnpSift -- snpsift version is 4.2 in the production pipeline
 # -------------------------------------------------------------------------------------------------
 # BFX Tools
-import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.0/unix/commands.wdl" as Unix
-import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.0/snpeff/SnpEff.wdl" as SnpEff
-import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.0/snpeff/SnpSift.wdl" as SnpSift
+import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.1/unix/commands.wdl" as Unix
+import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.1/snpeff/SnpEff.wdl" as SnpEff
+import "https://raw.githubusercontent.com/chopdgd/bfx-tools-wdl/v1.4.1/snpeff/SnpSift.wdl" as SnpSift
 
 workflow MitoAnnotation {
   input {