From 58c0da169b4b4f208e8c1f9a4298d60a4b6100bc Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:38:56 +0200
Subject: [PATCH] picard to 1.0
---
picard.wdl | 330 ++++++++++++++++++++++++++++-------------------------
1 file changed, 172 insertions(+), 158 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 444af3b..1095f4c 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -1,29 +1,32 @@
-task CollectMultipleMetrics {
- String? preCommand
- File bamFile
- File bamIndex
- File refFasta
- File refDict
- File refFastaIndex
- String basename
-
- # These should proably be optional, but I'm not sure how to handle the ouput in that
- # case (without a null literal).
- Boolean collectAlignmentSummaryMetrics = true
- Boolean collectInsertSizeMetrics = true
- Boolean qualityScoreDistribution = true
- Boolean meanQualityByCycle = true
- Boolean collectBaseDistributionByCycle = true
- Boolean collectGcBiasMetrics = true
- #Boolean? rnaSeqMetrics = false # There is a bug in picard https://github.com/broadinstitute/picard/issues/999
- Boolean collectSequencingArtifactMetrics = true
- Boolean collectQualityYieldMetrics = true
-
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
+version 1.0
+task CollectMultipleMetrics {
+ input {
+ String? preCommand
+ File bamFile
+ File bamIndex
+ File refFasta
+ File refDict
+ File refFastaIndex
+ String basename
+
+ # These should proably be optional, but I'm not sure how to handle the ouput in that
+ # case (without a null literal).
+ Boolean collectAlignmentSummaryMetrics = true
+ Boolean collectInsertSizeMetrics = true
+ Boolean qualityScoreDistribution = true
+ Boolean meanQualityByCycle = true
+ Boolean collectBaseDistributionByCycle = true
+ Boolean collectGcBiasMetrics = true
+ #Boolean? rnaSeqMetrics = false # There is a bug in picard https://github.com/broadinstitute/picard/issues/999
+ Boolean collectSequencingArtifactMetrics = true
+ Boolean collectQualityYieldMetrics = true
+
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
@@ -32,23 +35,23 @@ task CollectMultipleMetrics {
command {
set -e -o pipefail
- mkdir -p $(dirname "${basename}")
- ${preCommand}
- ${toolCommand} \
+ mkdir -p $(dirname "~{basename}")
+ ~{preCommand}
+ ~{toolCommand} \
CollectMultipleMetrics \
- I=${bamFile} \
- R=${refFasta} \
- O=${basename} \
+ I=~{bamFile} \
+ R=~{refFasta} \
+ O=~{basename} \
PROGRAM=null \
- ${true="PROGRAM=CollectAlignmentSummaryMetrics" false="" collectAlignmentSummaryMetrics} \
- ${true="PROGRAM=CollectInsertSizeMetrics" false="" collectInsertSizeMetrics} \
- ${true="PROGRAM=QualityScoreDistribution" false="" qualityScoreDistribution} \
- ${true="PROGRAM=MeanQualityByCycle" false="" meanQualityByCycle} \
- ${true="PROGRAM=CollectBaseDistributionByCycle" false="" collectBaseDistributionByCycle} \
- ${true="PROGRAM=CollectGcBiasMetrics" false="" collectGcBiasMetrics} \
- ${true="PROGRAM=CollectSequencingArtifactMetrics" false=""
+ ~{true="PROGRAM=CollectAlignmentSummaryMetrics" false="" collectAlignmentSummaryMetrics} \
+ ~{true="PROGRAM=CollectInsertSizeMetrics" false="" collectInsertSizeMetrics} \
+ ~{true="PROGRAM=QualityScoreDistribution" false="" qualityScoreDistribution} \
+ ~{true="PROGRAM=MeanQualityByCycle" false="" meanQualityByCycle} \
+ ~{true="PROGRAM=CollectBaseDistributionByCycle" false="" collectBaseDistributionByCycle} \
+ ~{true="PROGRAM=CollectGcBiasMetrics" false="" collectGcBiasMetrics} \
+ ~{true="PROGRAM=CollectSequencingArtifactMetrics" false=""
collectSequencingArtifactMetrics} \
- ${true="PROGRAM=CollectQualityYieldMetrics" false="" collectQualityYieldMetrics}
+ ~{true="PROGRAM=CollectQualityYieldMetrics" false="" collectQualityYieldMetrics}
}
output {
@@ -78,18 +81,19 @@ task CollectMultipleMetrics {
}
task CollectRnaSeqMetrics {
- String? preCommand
- File bamFile
- File bamIndex
- File refRefflat
- String basename
- String? strandSpecificity = "NONE"
-
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
-
+ input {
+ String? preCommand
+ File bamFile
+ File bamIndex
+ File refRefflat
+ String basename
+ String? strandSpecificity = "NONE"
+
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
@@ -98,15 +102,15 @@ task CollectRnaSeqMetrics {
command {
set -e -o pipefail
- mkdir -p $(dirname "${basename}")
- ${preCommand}
- ${toolCommand} \
+ mkdir -p $(dirname "~{basename}")
+ ~{preCommand}
+ ~{toolCommand} \
CollectRnaSeqMetrics \
- I=${bamFile} \
- O=${basename}.RNA_Metrics \
- CHART_OUTPUT=${basename}.RNA_Metrics.pdf \
- ${"STRAND_SPECIFICITY=" + strandSpecificity} \
- REF_FLAT=${refRefflat}
+ I=~{bamFile} \
+ O=~{basename}.RNA_Metrics \
+ CHART_OUTPUT=~{basename}.RNA_Metrics.pdf \
+ ~{"STRAND_SPECIFICITY=" + strandSpecificity} \
+ REF_FLAT=~{refRefflat}
}
output {
@@ -120,20 +124,22 @@ task CollectRnaSeqMetrics {
}
task CollectTargetedPcrMetrics {
- String? preCommand
- File bamFile
- File bamIndex
- File refFasta
- File refDict
- File refFastaIndex
- File ampliconIntervals
- Array[File]+ targetIntervals
- String basename
-
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File bamFile
+ File bamIndex
+ File refFasta
+ File refDict
+ File refFastaIndex
+ File ampliconIntervals
+ Array[File]+ targetIntervals
+ String basename
+
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
@@ -143,17 +149,17 @@ task CollectTargetedPcrMetrics {
command {
set -e -o pipefail
- mkdir -p $(dirname "${basename}")
- ${preCommand}
- ${toolCommand} \
+ mkdir -p $(dirname "~{basename}")
+ ~{preCommand}
+ ~{toolCommand} \
CollectTargetedPcrMetrics \
- I=${bamFile} \
- R=${refFasta} \
- AMPLICON_INTERVALS=${ampliconIntervals} \
- TARGET_INTERVALS=${sep=" TARGET_INTERVALS=" targetIntervals} \
- O=${basename}.targetPcrMetrics \
- PER_BASE_COVERAGE=${basename}.targetPcrPerBaseCoverage \
- PER_TARGET_COVERAGE=${basename}.targetPcrPerTargetCoverage
+ I=~{bamFile} \
+ R=~{refFasta} \
+ AMPLICON_INTERVALS=~{ampliconIntervals} \
+ TARGET_INTERVALS=~{sep=" TARGET_INTERVALS=" targetIntervals} \
+ O=~{basename}.targetPcrMetrics \
+ PER_BASE_COVERAGE=~{basename}.targetPcrPerBaseCoverage \
+ PER_TARGET_COVERAGE=~{basename}.targetPcrPerTargetCoverage
}
output {
@@ -169,14 +175,16 @@ task CollectTargetedPcrMetrics {
# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
task GatherBamFiles {
- String? preCommand
- Array[File]+ input_bams
- String output_bam_path
- Int? compression_level
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ Array[File]+ input_bams
+ String output_bam_path
+ Int? compression_level
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
@@ -186,19 +194,19 @@ task GatherBamFiles {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
GatherBamFiles \
- INPUT=${sep=' INPUT=' input_bams} \
- OUTPUT=${output_bam_path} \
+ INPUT=~{sep=' INPUT=' input_bams} \
+ OUTPUT=~{output_bam_path} \
CREATE_INDEX=true \
CREATE_MD5_FILE=true
}
output {
- File output_bam = "${output_bam_path}"
+ File output_bam = "~{output_bam_path}"
File output_bam_index = sub(output_bam_path, ".bam$", ".bai")
- File output_bam_md5 = "${output_bam_path}.md5"
+ File output_bam_md5 = "~{output_bam_path}.md5"
}
runtime {
@@ -208,21 +216,23 @@ task GatherBamFiles {
# Mark duplicate reads to avoid counting non-independent observations
task MarkDuplicates {
- String? preCommand
- Array[File] input_bams
- String output_bam_path
- String metrics_path
- Int? compression_level
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
-
- # The program default for READ_NAME_REGEX is appropriate in nearly every case.
- # Sometimes we wish to supply "null" in order to turn off optical duplicate detection
- # This can be desirable if you don't mind the estimated library size being wrong and optical duplicate detection is taking >7 days and failing
- String? read_name_regex
+ input {
+ String? preCommand
+ Array[File] input_bams
+ String output_bam_path
+ String metrics_path
+ Int? compression_level
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+
+ # The program default for READ_NAME_REGEX is appropriate in nearly every case.
+ # Sometimes we wish to supply "null" in order to turn off optical duplicate detection
+ # This can be desirable if you don't mind the estimated library size being wrong and optical duplicate detection is taking >7 days and failing
+ String? read_name_regex
+ }
# Task is assuming query-sorted input so that the Secondary and Supplementary reads get marked correctly
# This works because the output of BWA is query-grouped and therefore, so is the output of MergeBamAlignment.
# While query-grouped isn't actually query-sorted, it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname"
@@ -234,15 +244,15 @@ task MarkDuplicates {
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p $(dirname ${output_bam_path})
- ${toolCommand} \
+ ~{preCommand}
+ mkdir -p $(dirname ~{output_bam_path})
+ ~{toolCommand} \
MarkDuplicates \
- INPUT=${sep=' INPUT=' input_bams} \
- OUTPUT=${output_bam_path} \
- METRICS_FILE=${metrics_path} \
+ INPUT=~{sep=' INPUT=' input_bams} \
+ OUTPUT=~{output_bam_path} \
+ METRICS_FILE=~{metrics_path} \
VALIDATION_STRINGENCY=SILENT \
- ${"READ_NAME_REGEX=" + read_name_regex} \
+ ~{"READ_NAME_REGEX=" + read_name_regex} \
OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
CLEAR_DT="false" \
CREATE_INDEX=true \
@@ -262,16 +272,17 @@ task MarkDuplicates {
# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
task MergeVCFs {
- String? preCommand
- Array[File] inputVCFs
- Array[File] inputVCFsIndexes
- String outputVCFpath
- Int? compressionLevel
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
-
+ input {
+ String? preCommand
+ Array[File] inputVCFs
+ Array[File] inputVCFsIndexes
+ String outputVCFpath
+ Int? compressionLevel
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
# Using MergeVcfs instead of GatherVcfs so we can create indices
# See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
Int mem = ceil(select_first([memory, 4.0]))
@@ -282,11 +293,11 @@ task MergeVCFs {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
MergeVcfs \
- INPUT=${sep=' INPUT=' inputVCFs} \
- OUTPUT=${outputVCFpath}
+ INPUT=~{sep=' INPUT=' inputVCFs} \
+ OUTPUT=~{outputVCFpath}
}
output {
@@ -300,14 +311,16 @@ task MergeVCFs {
}
task SamToFastq {
- String? preCommand
- File inputBam
- String outputRead1
- String? outputRead2
- String? outputUnpaired
- String? picardJar
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputUnpaired
+ String? picardJar
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 16.0])) # High memory default to avoid crashes.
String toolCommand = if defined(picardJar)
@@ -316,13 +329,13 @@ task SamToFastq {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
SamToFastq \
- I=${inputBam} \
- ${"FASTQ=" + outputRead1} \
- ${"SECOND_END_FASTQ=" + outputRead2} \
- ${"UNPAIRED_FASTQ=" + outputUnpaired}
+ I=~{inputBam} \
+ ~{"FASTQ=" + outputRead1} \
+ ~{"SECOND_END_FASTQ=" + outputRead2} \
+ ~{"UNPAIRED_FASTQ=" + outputUnpaired}
}
output {
@@ -337,14 +350,15 @@ task SamToFastq {
}
task ScatterIntervalList {
- String? preCommand
- File interval_list
- Int scatter_count
- String? picardJar
-
- Float? memory
- Float? memoryMultiplier
-
+ input {
+ String? preCommand
+ File interval_list
+ Int scatter_count
+ String? picardJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
@@ -353,15 +367,15 @@ task ScatterIntervalList {
command {
set -e -o pipefail
- ${preCommand}
+ ~{preCommand}
mkdir scatter_list
- ${toolCommand} \
+ ~{toolCommand} \
IntervalListTools \
- SCATTER_COUNT=${scatter_count} \
+ SCATTER_COUNT=~{scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
UNIQUE=true \
SORT=true \
- INPUT=${interval_list} \
+ INPUT=~{interval_list} \
OUTPUT=scatter_list
}
--
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