From 84e80fd0c444ab151625bd95bd8ea7a3f4ce40d6 Mon Sep 17 00:00:00 2001 From: Yuuki Galaxy Date: Tue, 23 Mar 2021 10:45:04 +0800 Subject: [PATCH] sed -i -e 's/docker: dockerImage/#docker: dockerImage/g' new file: _edit.sh --- etc/gatk-wdl/fm2gatk/BamMetrics/tasks/common.wdl | 12 ++--- etc/gatk-wdl/fm2gatk/BamMetrics/tasks/picard.wdl | 28 +++++------ etc/gatk-wdl/fm2gatk/BamMetrics/tasks/samtools.wdl | 22 ++++----- etc/gatk-wdl/fm2gatk/QC/tasks/cutadapt.wdl | 2 +- etc/gatk-wdl/fm2gatk/QC/tasks/fastqc.wdl | 4 +- etc/gatk-wdl/fm2gatk/_edit.sh | 5 ++ .../fm2gatk/gatk-preprocess/tasks/gatk.wdl | 56 +++++++++++----------- .../fm2gatk/gatk-preprocess/tasks/picard.wdl | 28 +++++------ .../gatk-variantcalling/jointgenotyping.wdl | 2 +- .../single-sample-variantcalling.wdl | 2 +- .../fm2gatk/gatk-variantcalling/tasks/bcftools.wdl | 4 +- .../fm2gatk/gatk-variantcalling/tasks/bedtools.wdl | 10 ++-- .../gatk-variantcalling/tasks/chunked-scatter.wdl | 4 +- .../fm2gatk/gatk-variantcalling/tasks/gatk.wdl | 56 +++++++++++----------- .../fm2gatk/gatk-variantcalling/tasks/picard.wdl | 28 +++++------ .../structural-variantcalling/tasks/bcftools.wdl | 4 +- .../structural-variantcalling/tasks/bwa.wdl | 4 +- .../structural-variantcalling/tasks/clever.wdl | 4 +- .../structural-variantcalling/tasks/common.wdl | 12 ++--- .../structural-variantcalling/tasks/delly.wdl | 2 +- .../structural-variantcalling/tasks/manta.wdl | 4 +- .../structural-variantcalling/tasks/picard.wdl | 28 +++++------ .../structural-variantcalling/tasks/samtools.wdl | 22 ++++----- .../structural-variantcalling/tasks/smoove.wdl | 2 +- .../structural-variantcalling/tasks/survivor.wdl | 2 +- etc/gatk-wdl/fm2gatk/tasks/biowdl.wdl | 2 +- etc/gatk-wdl/fm2gatk/tasks/bwa.wdl | 4 +- etc/gatk-wdl/fm2gatk/tasks/chunked-scatter.wdl | 4 +- etc/gatk-wdl/fm2gatk/tasks/common.wdl | 12 ++--- etc/gatk-wdl/fm2gatk/tasks/multiqc.wdl | 2 +- etc/gatk-wdl/fm2gatk/tasks/sambamba.wdl | 6 +-- 31 files changed, 191 insertions(+), 186 deletions(-) create mode 100644 etc/gatk-wdl/fm2gatk/_edit.sh diff --git a/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/common.wdl b/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/common.wdl index e96cc1c81..273dde7dd 100644 --- a/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/common.wdl +++ b/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/common.wdl @@ -59,7 +59,7 @@ task CheckFileMD5 { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -111,7 +111,7 @@ task Copy { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -151,7 +151,7 @@ task MapMd5 { runtime { memory: "1G" - docker: dockerImage + #docker: dockerImage } } @@ -174,7 +174,7 @@ task StringArrayMd5 { runtime { memory: "1G" - docker: dockerImage + #docker: dockerImage } } @@ -204,7 +204,7 @@ task TextToFile { runtime { memory: "1G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } } @@ -237,7 +237,7 @@ task YamlToJson { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/picard.wdl b/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/picard.wdl index 1afa5ea72..76e46a3b6 100644 --- a/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/picard.wdl +++ b/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/picard.wdl @@ -47,7 +47,7 @@ task BedToIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -156,7 +156,7 @@ task CollectMultipleMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -226,7 +226,7 @@ task CollectRnaSeqMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -287,7 +287,7 @@ task CollectTargetedPcrMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -341,7 +341,7 @@ task CreateSequenceDictionary { runtime { memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -392,7 +392,7 @@ task GatherBamFiles { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -439,7 +439,7 @@ task GatherVcfs { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory time_minutes: timeMinutes } @@ -520,7 +520,7 @@ task MarkDuplicates { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -584,7 +584,7 @@ task MergeVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -640,7 +640,7 @@ task SamToFastq { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -674,7 +674,7 @@ task ScatterIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -720,7 +720,7 @@ task SortSam { cpu: 1 memory: "~{1 + XmxGb}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -763,7 +763,7 @@ task SortVcf { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -809,7 +809,7 @@ task RenameSample { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } diff --git a/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/samtools.wdl b/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/samtools.wdl index c155f0260..18338728b 100644 --- a/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/samtools.wdl +++ b/etc/gatk-wdl/fm2gatk/BamMetrics/tasks/samtools.wdl @@ -46,7 +46,7 @@ task BgzipAndIndex { runtime { time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -83,7 +83,7 @@ task Faidx { runtime { memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -141,7 +141,7 @@ task Fastq { runtime { cpu: threads memory: memory - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -192,7 +192,7 @@ task FilterShortReadsBam { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -227,7 +227,7 @@ task Flagstat { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -275,7 +275,7 @@ task Index { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -310,7 +310,7 @@ task Markdup { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -354,7 +354,7 @@ task Merge { runtime { cpu: threads - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -408,7 +408,7 @@ task Sort { runtime { cpu: 1 memory: "~{memoryGb}G" - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -455,7 +455,7 @@ task Tabix { runtime { time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -514,7 +514,7 @@ task View { cpu: threads memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/QC/tasks/cutadapt.wdl b/etc/gatk-wdl/fm2gatk/QC/tasks/cutadapt.wdl index 7faeaff1e..2812c54fb 100644 --- a/etc/gatk-wdl/fm2gatk/QC/tasks/cutadapt.wdl +++ b/etc/gatk-wdl/fm2gatk/QC/tasks/cutadapt.wdl @@ -169,7 +169,7 @@ task Cutadapt { cpu: cores memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/QC/tasks/fastqc.wdl b/etc/gatk-wdl/fm2gatk/QC/tasks/fastqc.wdl index 04b6813f3..18fb41fd7 100644 --- a/etc/gatk-wdl/fm2gatk/QC/tasks/fastqc.wdl +++ b/etc/gatk-wdl/fm2gatk/QC/tasks/fastqc.wdl @@ -96,7 +96,7 @@ task Fastqc { runtime { cpu: threads memory: memory - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -157,7 +157,7 @@ task GetConfiguration { runtime { memory: "2G" # Needs more than 1 to pull the docker image time_minute: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/_edit.sh b/etc/gatk-wdl/fm2gatk/_edit.sh new file mode 100644 index 000000000..3b9412caf --- /dev/null +++ b/etc/gatk-wdl/fm2gatk/_edit.sh @@ -0,0 +1,5 @@ +#/bin/sh + +find . -type f -exec grep -H 'docker: dockerImage' {} \; +find . -type f -exec sed -i -e 's/docker: dockerImage/#docker: dockerImage/g' {} \; + diff --git a/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/gatk.wdl b/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/gatk.wdl index e0209a0c4..81c31240c 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/gatk.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/gatk.wdl @@ -57,7 +57,7 @@ task AnnotateIntervals { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -124,7 +124,7 @@ task ApplyBQSR { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -190,7 +190,7 @@ task BaseRecalibrator { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -246,7 +246,7 @@ task CalculateContamination { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -289,7 +289,7 @@ task CallCopyRatioSegments { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -339,7 +339,7 @@ task CollectAllelicCounts { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -397,7 +397,7 @@ task CollectReadCounts { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -453,7 +453,7 @@ task CombineGVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -526,7 +526,7 @@ task CombineVariants { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -578,7 +578,7 @@ task CreateReadCountPanelOfNormals { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -628,7 +628,7 @@ task DenoiseReadCounts { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -692,7 +692,7 @@ task FilterMutectCalls { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -745,7 +745,7 @@ task GatherBqsrReports { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -794,7 +794,7 @@ task GenomicsDBImport { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -858,7 +858,7 @@ task GenotypeGVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -917,7 +917,7 @@ task GetPileupSummaries { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -995,7 +995,7 @@ task HaplotypeCaller { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -1056,7 +1056,7 @@ task LearnReadOrientationModel { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1095,7 +1095,7 @@ task MergeStats { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1158,7 +1158,7 @@ task ModelSegments { } runtime { - docker: dockerImage + #docker: dockerImage time_minute: timeMinutes memory: memory } @@ -1229,7 +1229,7 @@ task MuTect2 { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1297,7 +1297,7 @@ task PlotDenoisedCopyRatios { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1353,7 +1353,7 @@ task PlotModeledSegments { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1411,7 +1411,7 @@ task PreprocessIntervals { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1468,7 +1468,7 @@ task SelectVariants { } runtime { - docker: dockerImage + #docker: dockerImage time_minute: timeMinutes memory: memory } @@ -1527,7 +1527,7 @@ task SplitNCigarReads { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1604,7 +1604,7 @@ task VariantEval { runtime { cpu: 1 - docker: dockerImage + #docker: dockerImage memory: memory time_minutes: timeMinutes } @@ -1668,7 +1668,7 @@ task VariantFiltration { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } diff --git a/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/picard.wdl b/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/picard.wdl index 1afa5ea72..76e46a3b6 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/picard.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-preprocess/tasks/picard.wdl @@ -47,7 +47,7 @@ task BedToIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -156,7 +156,7 @@ task CollectMultipleMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -226,7 +226,7 @@ task CollectRnaSeqMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -287,7 +287,7 @@ task CollectTargetedPcrMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -341,7 +341,7 @@ task CreateSequenceDictionary { runtime { memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -392,7 +392,7 @@ task GatherBamFiles { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -439,7 +439,7 @@ task GatherVcfs { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory time_minutes: timeMinutes } @@ -520,7 +520,7 @@ task MarkDuplicates { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -584,7 +584,7 @@ task MergeVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -640,7 +640,7 @@ task SamToFastq { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -674,7 +674,7 @@ task ScatterIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -720,7 +720,7 @@ task SortSam { cpu: 1 memory: "~{1 + XmxGb}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -763,7 +763,7 @@ task SortVcf { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -809,7 +809,7 @@ task RenameSample { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/jointgenotyping.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/jointgenotyping.wdl index 3e516752c..c16200bba 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/jointgenotyping.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/jointgenotyping.wdl @@ -145,4 +145,4 @@ workflow JointGenotyping { dockerImages: { description: "specify which docker images should be used for running this pipeline", category: "advanced" } } -} \ No newline at end of file +} diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/single-sample-variantcalling.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/single-sample-variantcalling.wdl index ebd4632dc..9d0de147d 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/single-sample-variantcalling.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/single-sample-variantcalling.wdl @@ -216,4 +216,4 @@ workflow SingleSampleCalling { standardMinConfidenceThresholdForCalling: {description: "Minimum confidence treshold used by haplotype caller.", category: "advanced"} timeMinutes: {description: "The time in minutes expected for each haplotype caller task. Will be exposed as the time_minutes runtime attribute.", category: "advanced"} } -} \ No newline at end of file +} diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bcftools.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bcftools.wdl index 2677899be..fcd222a2d 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bcftools.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bcftools.wdl @@ -52,7 +52,7 @@ task View { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -135,7 +135,7 @@ task Stats { cpu: threads + 1 time_minutes: timeMinutes memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bedtools.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bedtools.wdl index c228d6c6f..f41d3df43 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bedtools.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/bedtools.wdl @@ -48,7 +48,7 @@ task Complement { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -82,7 +82,7 @@ task Merge { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -118,7 +118,7 @@ task MergeBedFiles { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { bedFiles: {description: "The bed files to merge.", category: "required"} @@ -166,7 +166,7 @@ task Sort { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -201,7 +201,7 @@ task Intersect { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/chunked-scatter.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/chunked-scatter.wdl index b54a7d2e9..9a0109d57 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/chunked-scatter.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/chunked-scatter.wdl @@ -51,7 +51,7 @@ task ChunkedScatter { cpu: 1 memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -98,7 +98,7 @@ task ScatterRegions { runtime { cpu: 1 memory: memory - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/gatk.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/gatk.wdl index e0209a0c4..81c31240c 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/gatk.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/gatk.wdl @@ -57,7 +57,7 @@ task AnnotateIntervals { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -124,7 +124,7 @@ task ApplyBQSR { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -190,7 +190,7 @@ task BaseRecalibrator { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -246,7 +246,7 @@ task CalculateContamination { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -289,7 +289,7 @@ task CallCopyRatioSegments { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -339,7 +339,7 @@ task CollectAllelicCounts { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -397,7 +397,7 @@ task CollectReadCounts { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -453,7 +453,7 @@ task CombineGVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -526,7 +526,7 @@ task CombineVariants { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -578,7 +578,7 @@ task CreateReadCountPanelOfNormals { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -628,7 +628,7 @@ task DenoiseReadCounts { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -692,7 +692,7 @@ task FilterMutectCalls { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -745,7 +745,7 @@ task GatherBqsrReports { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -794,7 +794,7 @@ task GenomicsDBImport { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -858,7 +858,7 @@ task GenotypeGVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -917,7 +917,7 @@ task GetPileupSummaries { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -995,7 +995,7 @@ task HaplotypeCaller { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -1056,7 +1056,7 @@ task LearnReadOrientationModel { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1095,7 +1095,7 @@ task MergeStats { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1158,7 +1158,7 @@ task ModelSegments { } runtime { - docker: dockerImage + #docker: dockerImage time_minute: timeMinutes memory: memory } @@ -1229,7 +1229,7 @@ task MuTect2 { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1297,7 +1297,7 @@ task PlotDenoisedCopyRatios { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1353,7 +1353,7 @@ task PlotModeledSegments { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1411,7 +1411,7 @@ task PreprocessIntervals { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1468,7 +1468,7 @@ task SelectVariants { } runtime { - docker: dockerImage + #docker: dockerImage time_minute: timeMinutes memory: memory } @@ -1527,7 +1527,7 @@ task SplitNCigarReads { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -1604,7 +1604,7 @@ task VariantEval { runtime { cpu: 1 - docker: dockerImage + #docker: dockerImage memory: memory time_minutes: timeMinutes } @@ -1668,7 +1668,7 @@ task VariantFiltration { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } diff --git a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/picard.wdl b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/picard.wdl index 1afa5ea72..76e46a3b6 100644 --- a/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/picard.wdl +++ b/etc/gatk-wdl/fm2gatk/gatk-variantcalling/tasks/picard.wdl @@ -47,7 +47,7 @@ task BedToIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -156,7 +156,7 @@ task CollectMultipleMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -226,7 +226,7 @@ task CollectRnaSeqMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -287,7 +287,7 @@ task CollectTargetedPcrMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -341,7 +341,7 @@ task CreateSequenceDictionary { runtime { memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -392,7 +392,7 @@ task GatherBamFiles { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -439,7 +439,7 @@ task GatherVcfs { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory time_minutes: timeMinutes } @@ -520,7 +520,7 @@ task MarkDuplicates { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -584,7 +584,7 @@ task MergeVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -640,7 +640,7 @@ task SamToFastq { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -674,7 +674,7 @@ task ScatterIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -720,7 +720,7 @@ task SortSam { cpu: 1 memory: "~{1 + XmxGb}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -763,7 +763,7 @@ task SortVcf { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -809,7 +809,7 @@ task RenameSample { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bcftools.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bcftools.wdl index 2677899be..fcd222a2d 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bcftools.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bcftools.wdl @@ -52,7 +52,7 @@ task View { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -135,7 +135,7 @@ task Stats { cpu: threads + 1 time_minutes: timeMinutes memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bwa.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bwa.wdl index 58e1dc803..7e58e8651 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bwa.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/bwa.wdl @@ -71,7 +71,7 @@ task Mem { cpu: threads memory: "~{select_first([memoryGb, estimatedMemoryGb])}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -150,7 +150,7 @@ task Kit { cpu: threads memory: "~{select_first([memoryGb, estimatedMemoryGb])}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/clever.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/clever.wdl index 3a6515f72..e9eeac2e2 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/clever.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/clever.wdl @@ -65,7 +65,7 @@ task Mateclever { cpu: threads memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -119,7 +119,7 @@ task Prediction { cpu: threads memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/common.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/common.wdl index e96cc1c81..273dde7dd 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/common.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/common.wdl @@ -59,7 +59,7 @@ task CheckFileMD5 { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -111,7 +111,7 @@ task Copy { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -151,7 +151,7 @@ task MapMd5 { runtime { memory: "1G" - docker: dockerImage + #docker: dockerImage } } @@ -174,7 +174,7 @@ task StringArrayMd5 { runtime { memory: "1G" - docker: dockerImage + #docker: dockerImage } } @@ -204,7 +204,7 @@ task TextToFile { runtime { memory: "1G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } } @@ -237,7 +237,7 @@ task YamlToJson { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/delly.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/delly.wdl index efa1bf60d..47c8378a6 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/delly.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/delly.wdl @@ -51,7 +51,7 @@ task CallSV { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/manta.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/manta.wdl index 5382d2a5b..6c46406dc 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/manta.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/manta.wdl @@ -60,7 +60,7 @@ task Germline { runtime { cpu: cores memory: "~{memoryGb}G" - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -133,7 +133,7 @@ task Somatic { runtime { cpu: cores memory: "~{memoryGb}G" - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/picard.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/picard.wdl index 1afa5ea72..76e46a3b6 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/picard.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/picard.wdl @@ -47,7 +47,7 @@ task BedToIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -156,7 +156,7 @@ task CollectMultipleMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -226,7 +226,7 @@ task CollectRnaSeqMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -287,7 +287,7 @@ task CollectTargetedPcrMetrics { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -341,7 +341,7 @@ task CreateSequenceDictionary { runtime { memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -392,7 +392,7 @@ task GatherBamFiles { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -439,7 +439,7 @@ task GatherVcfs { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory time_minutes: timeMinutes } @@ -520,7 +520,7 @@ task MarkDuplicates { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: "~{memoryMb}M" } @@ -584,7 +584,7 @@ task MergeVCFs { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -640,7 +640,7 @@ task SamToFastq { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -674,7 +674,7 @@ task ScatterIntervalList { } runtime { - docker: dockerImage + #docker: dockerImage memory: memory } } @@ -720,7 +720,7 @@ task SortSam { cpu: 1 memory: "~{1 + XmxGb}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -763,7 +763,7 @@ task SortVcf { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } @@ -809,7 +809,7 @@ task RenameSample { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes memory: memory } diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/samtools.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/samtools.wdl index c155f0260..18338728b 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/samtools.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/samtools.wdl @@ -46,7 +46,7 @@ task BgzipAndIndex { runtime { time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -83,7 +83,7 @@ task Faidx { runtime { memory: memory - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -141,7 +141,7 @@ task Fastq { runtime { cpu: threads memory: memory - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -192,7 +192,7 @@ task FilterShortReadsBam { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -227,7 +227,7 @@ task Flagstat { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -275,7 +275,7 @@ task Index { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -310,7 +310,7 @@ task Markdup { } runtime { - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -354,7 +354,7 @@ task Merge { runtime { cpu: threads - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -408,7 +408,7 @@ task Sort { runtime { cpu: 1 memory: "~{memoryGb}G" - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -455,7 +455,7 @@ task Tabix { runtime { time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -514,7 +514,7 @@ task View { cpu: threads memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/smoove.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/smoove.wdl index e8846f72b..5c7bed9e2 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/smoove.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/smoove.wdl @@ -52,7 +52,7 @@ task Call { runtime { memory: memory - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } diff --git a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/survivor.wdl b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/survivor.wdl index e5ac7b5bf..e0fc48fa2 100644 --- a/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/survivor.wdl +++ b/etc/gatk-wdl/fm2gatk/structural-variantcalling/tasks/survivor.wdl @@ -59,7 +59,7 @@ task Merge { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/tasks/biowdl.wdl b/etc/gatk-wdl/fm2gatk/tasks/biowdl.wdl index 838755d91..619f8ca58 100644 --- a/etc/gatk-wdl/fm2gatk/tasks/biowdl.wdl +++ b/etc/gatk-wdl/fm2gatk/tasks/biowdl.wdl @@ -54,7 +54,7 @@ task InputConverter { runtime { memory: "128M" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/tasks/bwa.wdl b/etc/gatk-wdl/fm2gatk/tasks/bwa.wdl index 58e1dc803..7e58e8651 100644 --- a/etc/gatk-wdl/fm2gatk/tasks/bwa.wdl +++ b/etc/gatk-wdl/fm2gatk/tasks/bwa.wdl @@ -71,7 +71,7 @@ task Mem { cpu: threads memory: "~{select_first([memoryGb, estimatedMemoryGb])}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -150,7 +150,7 @@ task Kit { cpu: threads memory: "~{select_first([memoryGb, estimatedMemoryGb])}G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/tasks/chunked-scatter.wdl b/etc/gatk-wdl/fm2gatk/tasks/chunked-scatter.wdl index b54a7d2e9..9a0109d57 100644 --- a/etc/gatk-wdl/fm2gatk/tasks/chunked-scatter.wdl +++ b/etc/gatk-wdl/fm2gatk/tasks/chunked-scatter.wdl @@ -51,7 +51,7 @@ task ChunkedScatter { cpu: 1 memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -98,7 +98,7 @@ task ScatterRegions { runtime { cpu: 1 memory: memory - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } diff --git a/etc/gatk-wdl/fm2gatk/tasks/common.wdl b/etc/gatk-wdl/fm2gatk/tasks/common.wdl index e96cc1c81..273dde7dd 100644 --- a/etc/gatk-wdl/fm2gatk/tasks/common.wdl +++ b/etc/gatk-wdl/fm2gatk/tasks/common.wdl @@ -59,7 +59,7 @@ task CheckFileMD5 { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -111,7 +111,7 @@ task Copy { } runtime { - docker: dockerImage + #docker: dockerImage } } @@ -151,7 +151,7 @@ task MapMd5 { runtime { memory: "1G" - docker: dockerImage + #docker: dockerImage } } @@ -174,7 +174,7 @@ task StringArrayMd5 { runtime { memory: "1G" - docker: dockerImage + #docker: dockerImage } } @@ -204,7 +204,7 @@ task TextToFile { runtime { memory: "1G" time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } } @@ -237,7 +237,7 @@ task YamlToJson { runtime { memory: memory time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/tasks/multiqc.wdl b/etc/gatk-wdl/fm2gatk/tasks/multiqc.wdl index 7dcf333eb..03f7fafb7 100644 --- a/etc/gatk-wdl/fm2gatk/tasks/multiqc.wdl +++ b/etc/gatk-wdl/fm2gatk/tasks/multiqc.wdl @@ -134,7 +134,7 @@ task MultiQC { runtime { memory: select_first([memory, "~{memoryGb}G"]) time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { diff --git a/etc/gatk-wdl/fm2gatk/tasks/sambamba.wdl b/etc/gatk-wdl/fm2gatk/tasks/sambamba.wdl index cd8da21e5..63ccc9cd5 100644 --- a/etc/gatk-wdl/fm2gatk/tasks/sambamba.wdl +++ b/etc/gatk-wdl/fm2gatk/tasks/sambamba.wdl @@ -70,7 +70,7 @@ task Markdup { memory: "~{memoryMb}M" cpu: threads time_minutes: timeMinutes - docker: dockerImage + #docker: dockerImage } parameter_meta { @@ -130,7 +130,7 @@ task Sort { runtime { cpu: threads memory: "~{memoryGb}G" - docker: dockerImage + #docker: dockerImage time_minutes: timeMinutes } @@ -148,4 +148,4 @@ task Sort { # outputs outputBam: {description: "Sorted BAM file."} } -} \ No newline at end of file +} -- 2.11.4.GIT