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biowdl
tasks
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624826f7
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624826f7
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5 years ago
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Cats
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add parameter_meta to picard metrics
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CHANGELOG.md
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CHANGELOG.md
picard.wdl
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88 additions, 2 deletions
picard.wdl
scripts
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CHANGELOG.md
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@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 2.2.0-dev
---------------------------
+
Added parameter_meta sections to a variety of tasks.
+
Picard's BedToIntervalList outputPath ipnut is now optional (with a default of "regions.interval_list")
+
Update htseq to default image version 0.11.2
+
Update biowdl-input-converter in common.wdl to version 0.2.1.
+
Update TALON section to now include the new annotation file output, and add config file creation to the TALON task.
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picard.wdl
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@@ -4,7 +4,7 @@ task BedToIntervalList {
input {
File bedFile
File dict
String outputPath
String outputPath
= "regions.interval_list"
String memory = "12G"
String javaXmx = "4G"
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@@ -29,6 +29,18 @@ task BedToIntervalList {
docker: dockerImage
memory: memory
}
parameter_meta {
bedfile: {description: "A bed file", category: "required"}
dict: {description: "A sequence dict file.", category: "required"}
outputPath: {description: "The location the output interval list should be written to.",
category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CollectMultipleMetrics {
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@@ -119,10 +131,44 @@ task CollectMultipleMetrics {
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBam: {description: "The input BAM file for which metrics will be collected.",
category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
basename: {description: "The basename/prefix of the output files (may include directories).",
category: "required"}
collectAlignmentSummaryMetrics: {description: "Equivalent to the `PROGRAM=CollectAlignmentSummaryMetrics` argument.",
category: "common"}
collectInsertSizeMetrics: {description: "Equivalent to the `PROGRAM=CollectInsertSizeMetrics` argument.",
category: "common"}
qualityScoreDistribution: {description: "Equivalent to the `PROGRAM=QualityScoreDistribution` argument.",
category: "common"}
meanQualityByCycle: {description: "Equivalent to the `PROGRAM=MeanQualityByCycle` argument.",
category: "common"}
collectBaseDistributionByCycle: {description: "Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` argument.",
category: "common"}
collectGcBiasMetrics: {description: "Equivalent to the `PROGRAM=CollectGcBiasMetrics` argument.",
category: "common"}
collectSequencingArtifactMetrics: {description: "Equivalent to the `PROGRAM=CollectSequencingArtifactMetrics` argument.",
category: "common"}
collectQualityYieldMetrics: {description: "Equivalent to the `PROGRAM=CollectQualityYieldMetrics` argument.",
category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CollectRnaSeqMetrics {
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@@ -159,6 +205,23 @@ task CollectRnaSeqMetrics {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBam: {description: "The input BAM file for which metrics will be collected.",
category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
refRefflat: {description: "A refflat file containing gene annotations", catehory: "required"}
basename: {description: "The basename/prefix of the output files (may include directories).",
category: "required"}
strandSpecificity: {description: "Equivalent to the `STRAND_SPECIFICITY` option of picard's CollectRnaSeqMetrics",
category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CollectTargetedPcrMetrics {
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@@ -201,6 +264,29 @@ task CollectTargetedPcrMetrics {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBam: {description: "The input BAM file for which metrics will be collected.",
category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
ampliconIntervals: {description: "An interval list describinig the coordinates of the amplicons sequenced.",
category: "required"}
targetIntervals: {description: "An interval list describing the coordinates of the targets sequenced.",
category: "required"}
basename: {description: "The basename/prefix of the output files (may include directories).",
category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
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