diff --git a/gatk.wdl b/gatk.wdl index b72d9a61c708d4b06c8ff415d6b584285641c718..6e56e3dfb693d566d8a0b21bd47aa3befcfa3fe9 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -15,6 +15,7 @@ task ApplyBQSR { Int memory = 4 Float memoryMultiplier = 3.0 + String dockerTag = "3.8--5" } String toolCommand = if defined(gatkJar) @@ -48,6 +49,7 @@ task ApplyBQSR { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -66,6 +68,7 @@ task BaseRecalibrator { Reference reference Int memory = 4 Float memoryMultiplier = 3.0 + String dockerTag = "3.8--5" } Array[File]+ knownIndelsSitesVCFsArg = flatten([ @@ -95,6 +98,7 @@ task BaseRecalibrator { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -114,6 +118,7 @@ task CombineGVCFs { Int memory = 4 Float memoryMultiplier = 3.0 + String dockerTag = "3.8--5" } String toolCommand = if defined(gatkJar) @@ -139,6 +144,7 @@ task CombineGVCFs { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -153,6 +159,7 @@ task GatherBqsrReports { Int memory = 4 Float memoryMultiplier = 3.0 + String dockerTag = "3.8--5" } String toolCommand = if defined(gatkJar) @@ -173,6 +180,7 @@ task GatherBqsrReports { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -194,6 +202,7 @@ task GenotypeGVCFs { Int memory = 6 Float memoryMultiplier = 2.0 + String dockerTag = "3.8--5" } File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else "" @@ -224,7 +233,8 @@ task GenotypeGVCFs { } } - runtime{ + runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -245,6 +255,7 @@ task HaplotypeCallerGvcf { Int memory = 4 Float memoryMultiplier = 3 + String dockerTag = "3.8--5" } File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else "" @@ -275,6 +286,7 @@ task HaplotypeCallerGvcf { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -294,6 +306,7 @@ task MuTect2 { String? gatkJar Int memory = 4 Float memoryMultiplier = 3 + String dockerTag = "3.8--5" } String toolCommand = if defined(gatkJar) @@ -321,6 +334,7 @@ task MuTect2 { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } } @@ -337,6 +351,7 @@ task SplitNCigarReads { Int memory = 4 Float memoryMultiplier = 4 + String dockerTag = "3.8--5" } String toolCommand = if defined(gatkJar) @@ -362,6 +377,7 @@ task SplitNCigarReads { } runtime { + docker: "quay.io/biocontainers/gatk:" + dockerTag memory: ceil(memory * memoryMultiplier) } }