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Commit c248c5bb authored by JasperBoom's avatar JasperBoom
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Update output names for the first set of tasks.

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CHANGELOG.md
+ 2
− 0
View file @ c248c5bb
...@@ -11,6 +11,8 @@ that users understand how the changes affect the new version. ...@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 4.0.0-develop version 4.0.0-develop
--------------------------- ---------------------------
+ Renamed outputs of tasks used in the TALON-WDL, PacBio-subreads-processing &
sequence-classification pipelines.
+ Reworked bcf2vcf task into bcftools view task. + Reworked bcf2vcf task into bcftools view task.
+ Removed the redundant format flag from the htseq interface. This is + Removed the redundant format flag from the htseq interface. This is
autodetected in newer versions of htseq. autodetected in newer versions of htseq.
......
ccs.wdl
+ 9
− 9
View file @ c248c5bb
...@@ -55,10 +55,10 @@ task CCS { ...@@ -55,10 +55,10 @@ task CCS {
} }
output { output {
File outputCCSfile = outputPrefix + ".ccs.bam" File ccsBam = outputPrefix + ".ccs.bam"
File outputCCSindexFile = outputPrefix + ".ccs.bam.pbi" File ccsBamIndex = outputPrefix + ".ccs.bam.pbi"
File outputReportFile = outputPrefix + ".ccs.report.txt" File ccsReport = outputPrefix + ".ccs.report.txt"
File outputSTDERRfile = outputPrefix + ".ccs.stderr.log" File ccsStderr = outputPrefix + ".ccs.stderr.log"
} }
runtime { runtime {
...@@ -70,7 +70,7 @@ task CCS { ...@@ -70,7 +70,7 @@ task CCS {
parameter_meta { parameter_meta {
# inputs # inputs
minPasses: {description: "Minimum number of full-length subreads required to generate CCS for a ZMW.", category: "advanced"} minPasses: {description: "Minimum number of full-length subreads required to generate ccs for a ZMW.", category: "advanced"}
minLength: {description: "Minimum draft length before polishing.", category: "advanced"} minLength: {description: "Minimum draft length before polishing.", category: "advanced"}
maxLength: {description: "Maximum draft length before polishing.", category: "advanced"} maxLength: {description: "Maximum draft length before polishing.", category: "advanced"}
byStrand: {description: "Generate a consensus for each strand.", category: "advanced"} byStrand: {description: "Generate a consensus for each strand.", category: "advanced"}
...@@ -84,9 +84,9 @@ task CCS { ...@@ -84,9 +84,9 @@ task CCS {
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"} 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"}
# outputs # outputs
outputCCSfile: {description: "Consensus reads output file."} ccsBam: {description: "Consensus reads output file."}
outputCCSindexFile: {description: "Index of consensus reads output file."} ccsBamIndex: {description: "Index of consensus reads output file."}
outputReportFile: {description: "CCS results report file."} ccsReport: {description: "Ccs results report file."}
outputSTDERRfile: {description: "CCS STDERR log file."} ccsStderr: {description: "Ccs STDERR log file."}
} }
} }
centrifuge.wdl
+ 21
− 21
View file @ c248c5bb
...@@ -59,7 +59,7 @@ task Build { ...@@ -59,7 +59,7 @@ task Build {
} }
output { output {
Array[File] outputIndex = glob(outputPrefix + "/" + indexBasename + "*.cf") Array[File] index = glob(outputPrefix + "/" + indexBasename + "*.cf")
} }
runtime { runtime {
...@@ -75,7 +75,7 @@ task Build { ...@@ -75,7 +75,7 @@ task Build {
conversionTable: {description: "List of UIDs (unique ID) and corresponding taxonomic IDs.", category: "required"} conversionTable: {description: "List of UIDs (unique ID) and corresponding taxonomic IDs.", category: "required"}
taxonomyTree: {description: "Taxonomic tree (e.g. nodes.dmp).", category: "required"} taxonomyTree: {description: "Taxonomic tree (e.g. nodes.dmp).", category: "required"}
nameTable: {description: "Name table (e.g. names.dmp).", category: "required"} nameTable: {description: "Name table (e.g. names.dmp).", category: "required"}
referenceFile: {description: "A comma-separated list of FASTA files containing the reference sequences to be aligned to.", category: "required"} referenceFile: {description: "A comma-separated list of fasta files containing the reference sequences to be aligned to.", category: "required"}
indexBasename: {description: "The basename of the index files to write.", category: "required"} indexBasename: {description: "The basename of the index files to write.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
offrate: {description: "The number of rows marked by the indexer.", category: "common"} offrate: {description: "The number of rows marked by the indexer.", category: "common"}
...@@ -88,7 +88,7 @@ task Build { ...@@ -88,7 +88,7 @@ task Build {
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"} 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"}
# outputs # outputs
outputIndex: {description: "Generated Centrifuge index."} index: {description: "Generated centrifuge index."}
} }
} }
...@@ -142,9 +142,9 @@ task Classify { ...@@ -142,9 +142,9 @@ task Classify {
>>> >>>
output { output {
File outputMetrics = outputPrefix + "_alignment_metrics.tsv" File metrics = outputPrefix + "_alignment_metrics.tsv"
File outputClassification = outputPrefix + "_classification.tsv" File classification = outputPrefix + "_classification.tsv"
File outputReport = outputPrefix + "_output_report.tsv" File report = outputPrefix + "_output_report.tsv"
} }
runtime { runtime {
...@@ -156,7 +156,7 @@ task Classify { ...@@ -156,7 +156,7 @@ task Classify {
parameter_meta { parameter_meta {
# inputs # inputs
inputFormat: {description: "The format of the read file(s).", category: "required"} inputFormat: {description: "The format of the read file(s).", category: "required"}
phred64: {description: "If set to true, Phred+64 encoding is used.", category: "required"} phred64: {description: "If set to true, phred+64 encoding is used.", category: "required"}
minHitLength: {description: "Minimum length of partial hits.", category: "required"} minHitLength: {description: "Minimum length of partial hits.", category: "required"}
indexFiles: {description: "The files of the index for the reference genomes.", category: "required"} indexFiles: {description: "The files of the index for the reference genomes.", category: "required"}
read1: {description: "List of files containing mate 1s, or unpaired reads.", category: "required"} read1: {description: "List of files containing mate 1s, or unpaired reads.", category: "required"}
...@@ -172,9 +172,9 @@ task Classify { ...@@ -172,9 +172,9 @@ task Classify {
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"} 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"}
# outputs # outputs
outputMetrics: {description: "File with Centrifuge metrics."} metrics: {description: "File with centrifuge metrics."}
outputClassification: {description: "File with the classification results."} classification: {description: "File with the classification results."}
outputReport: {description: "File with a classification summary."} report: {description: "File with a classification summary."}
} }
} }
...@@ -209,7 +209,7 @@ task Inspect { ...@@ -209,7 +209,7 @@ task Inspect {
>>> >>>
output { output {
File outputInspect = outputPrefix + "/" + printOption File inspectResult = outputPrefix + "/" + printOption
} }
runtime { runtime {
...@@ -223,13 +223,13 @@ task Inspect { ...@@ -223,13 +223,13 @@ task Inspect {
printOption: {description: "The output option for inspect (fasta, summary, conversionTable, taxonomyTree, nameTable, sizeTable)", category: "required"} printOption: {description: "The output option for inspect (fasta, summary, conversionTable, taxonomyTree, nameTable, sizeTable)", category: "required"}
indexFiles: {description: "The files of the index for the reference genomes.", category: "required"} indexFiles: {description: "The files of the index for the reference genomes.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
across: {description: "When printing FASTA output, output a newline character every <int> bases.", category: "common"} across: {description: "When printing fasta output, output a newline character every <int> bases.", category: "common"}
memory: {description: "The amount of memory available to the job.", category: "advanced"} memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"} 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"}
# outputs # outputs
outputInspect: {description: "Output file according to output option."} inspectResult: {description: "Output file according to output option."}
} }
} }
...@@ -300,7 +300,7 @@ task DownloadTaxonomy { ...@@ -300,7 +300,7 @@ task DownloadTaxonomy {
} }
} }
task Kreport { task KReport {
input { input {
File centrifugeClassification File centrifugeClassification
String outputPrefix String outputPrefix
...@@ -337,7 +337,7 @@ task Kreport { ...@@ -337,7 +337,7 @@ task Kreport {
>>> >>>
output { output {
File outputKreport = outputPrefix + "_kreport.tsv" File KReport = outputPrefix + "_kreport.tsv"
} }
runtime { runtime {
...@@ -348,10 +348,10 @@ task Kreport { ...@@ -348,10 +348,10 @@ task Kreport {
parameter_meta { parameter_meta {
# inputs # inputs
centrifugeClassification: {description: "File with Centrifuge classification results.", category: "required"} centrifugeClassification: {description: "File with centrifuge classification results.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
indexFiles: {description: "The files of the index for the reference genomes.", category: "required"} indexFiles: {description: "The files of the index for the reference genomes.", category: "required"}
noLCA: {description: "Do not report the LCA of multiple assignments, but report count fractions at the taxa.", category: "advanced"} noLCA: {description: "Do not report the lca of multiple assignments, but report count fractions at the taxa.", category: "advanced"}
showZeros: {description: "Show clades that have zero reads.", category: "advanced"} showZeros: {description: "Show clades that have zero reads.", category: "advanced"}
isCountTable: {description: "The format of the file is taxID<tab>COUNT.", category: "advanced"} isCountTable: {description: "The format of the file is taxID<tab>COUNT.", category: "advanced"}
minimumScore: {description: "Require a minimum score for reads to be counted.", category: "advanced"} minimumScore: {description: "Require a minimum score for reads to be counted.", category: "advanced"}
...@@ -361,7 +361,7 @@ task Kreport { ...@@ -361,7 +361,7 @@ task Kreport {
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"} 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"}
# outputs # outputs
outputKreport: {description: "File with kraken style report."} KReport: {description: "File with kraken style report."}
} }
} }
...@@ -384,7 +384,7 @@ task KTimportTaxonomy { ...@@ -384,7 +384,7 @@ task KTimportTaxonomy {
} }
output { output {
File outputKronaPlot = outputPrefix + "_krona.html" File kronaPlot = outputPrefix + "_krona.html"
} }
runtime { runtime {
...@@ -395,13 +395,13 @@ task KTimportTaxonomy { ...@@ -395,13 +395,13 @@ task KTimportTaxonomy {
parameter_meta { parameter_meta {
# inputs # inputs
inputFile: {description: "File with Centrifuge classification results.", category: "required"} inputFile: {description: "File with centrifuge classification results.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"} memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"} 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"}
# outputs # outputs
outputKronaPlot: {description: "Krona taxonomy plot html file."} kronaPlot: {description: "Krona taxonomy plot html file."}
} }
} }
isoseq3.wdl
+ 14
− 14
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...@@ -51,12 +51,12 @@ task Refine { ...@@ -51,12 +51,12 @@ task Refine {
} }
output { output {
File outputFLNCfile = outputDir + "/" + outputNamePrefix + ".bam" File refineBam = outputDir + "/" + outputNamePrefix + ".bam"
File outputFLNCindexFile = outputDir + "/" + outputNamePrefix + ".bam.pbi" File refineBamIndex = outputDir + "/" + outputNamePrefix + ".bam.pbi"
File outputConsensusReadsetFile = outputDir + "/" + outputNamePrefix + ".consensusreadset.xml" File refineConsensusReadset = outputDir + "/" + outputNamePrefix + ".consensusreadset.xml"
File outputFilterSummaryFile = outputDir + "/" + outputNamePrefix + ".filter_summary.json" File refineFilterSummary = outputDir + "/" + outputNamePrefix + ".filter_summary.json"
File outputReportFile = outputDir + "/" + outputNamePrefix + ".report.csv" File refineReport = outputDir + "/" + outputNamePrefix + ".report.csv"
File outputSTDERRfile = outputDir + "/" + outputNamePrefix + ".stderr.log" File refineStderr = outputDir + "/" + outputNamePrefix + ".stderr.log"
} }
runtime { runtime {
...@@ -69,9 +69,9 @@ task Refine { ...@@ -69,9 +69,9 @@ task Refine {
parameter_meta { parameter_meta {
# inputs # inputs
minPolyAlength: {description: "Minimum poly(A) tail length.", category: "advanced"} minPolyAlength: {description: "Minimum poly(A) tail length.", category: "advanced"}
requirePolyA: {description: "Require FL reads to have a poly(A) tail and remove it.", category: "common"} requirePolyA: {description: "Require fl reads to have a poly(A) tail and remove it.", category: "common"}
logLevel: {description: "Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).", category: "advanced"} logLevel: {description: "Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).", category: "advanced"}
inputBamFile: {description: "BAM input file.", category: "required"} inputBamFile: {description: "Bam input file.", category: "required"}
primerFile: {description: "Barcode/primer fasta file.", category: "required"} primerFile: {description: "Barcode/primer fasta file.", category: "required"}
outputDir: {description: "Output directory path.", category: "required"} outputDir: {description: "Output directory path.", category: "required"}
outputNamePrefix: {description: "Basename of the output files.", category: "required"} outputNamePrefix: {description: "Basename of the output files.", category: "required"}
...@@ -81,11 +81,11 @@ task Refine { ...@@ -81,11 +81,11 @@ task Refine {
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"} 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"}
# outputs # outputs
outputFLNCfile: {description: "Filtered reads output file."} refineBam: {description: "Filtered reads output file."}
outputFLNCindexFile: {description: "Index of filtered reads output file."} refineBamIndex: {description: "Index of filtered reads output file."}
outputSTDERRfile: {description: "Refine STDERR log file."} refineConsensusReadset: {description: "Refine consensus readset xml file."}
outputConsensusReadsetFile: {description: "Refine consensus readset XML file."} refineFilterSummary: {description: "Refine summary file."}
outputFilterSummaryFile: {description: "Refine summary file."} refineReport: {description: "Refine report file."}
outputReportFile: {description: "Refine report file."} refineStderr: {description: "Refine stderr log file."}
} }
} }
lima.wdl
+ 19
− 19
View file @ c248c5bb
...@@ -98,14 +98,14 @@ task Lima { ...@@ -98,14 +98,14 @@ task Lima {
} }
output { output {
Array[File] outputFLfile = glob("*.bam") Array[File] limaBam = glob("*.bam")
Array[File] outputFLindexFile = glob("*.bam.pbi") Array[File] limaBamIndex = glob("*.bam.pbi")
Array[File] outputFLxmlFile = glob("*.subreadset.xml") Array[File] limaXml = glob("*.subreadset.xml")
File outputSTDERRfile = outputPrefix + ".fl.stderr.log" File limaStderr = outputPrefix + ".fl.stderr.log"
File outputJSONfile = outputPrefix + ".fl.json" File limaJson = outputPrefix + ".fl.json"
File outputCountsFile = outputPrefix + ".fl.lima.counts" File limaCounts = outputPrefix + ".fl.lima.counts"
File outputReportFile = outputPrefix + ".fl.lima.report" File limaReport = outputPrefix + ".fl.lima.report"
File outputSummaryFile = outputPrefix + ".fl.lima.summary" File limaSummary = outputPrefix + ".fl.lima.summary"
} }
runtime { runtime {
...@@ -131,15 +131,15 @@ task Lima { ...@@ -131,15 +131,15 @@ task Lima {
minEndScore: {description: "Minimum end barcode score threshold is applied to the individual leading and trailing ends.", category: "advanced"} minEndScore: {description: "Minimum end barcode score threshold is applied to the individual leading and trailing ends.", category: "advanced"}
minSignalIncrease: {description: "The minimal score difference, between first and combined, required to call a barcode pair different.", category: "advanced"} minSignalIncrease: {description: "The minimal score difference, between first and combined, required to call a barcode pair different.", category: "advanced"}
minScoreLead: {description: "The minimal score lead required to call a barcode pair significant.", category: "common"} minScoreLead: {description: "The minimal score lead required to call a barcode pair significant.", category: "common"}
ccsMode: {description: "CCS mode, use optimal alignment options.", category: "common"} ccsMode: {description: "Ccs mode, use optimal alignment options.", category: "common"}
splitBamNamed: {description: "Split BAM output by resolved barcode pair name.", category: "common"} splitBamNamed: {description: "Split bam output by resolved barcode pair name.", category: "common"}
scoredAdapterRatio: {description: "Minimum ratio of scored vs sequenced adapters.", category: "advanced"} scoredAdapterRatio: {description: "Minimum ratio of scored vs sequenced adapters.", category: "advanced"}
peek: {description: "Demux the first N ZMWs and return the mean score, 0 means peeking deactivated.", category: "advanced"} peek: {description: "Demux the first N ZMWs and return the mean score, 0 means peeking deactivated.", category: "advanced"}
guess: {description: "Try to guess the used barcodes, using the provided mean score threshold, 0 means guessing deactivated.", category: "advanced"} guess: {description: "Try to guess the used barcodes, using the provided mean score threshold, 0 means guessing deactivated.", category: "advanced"}
guessMinCount: {description: "Minimum number of ZMWs observed to whitelist barcodes.", category: "advanced"} guessMinCount: {description: "Minimum number of ZMWs observed to whitelist barcodes.", category: "advanced"}
peekGuess: {description: "Try to infer the used barcodes subset, by peeking at the first 50,000 ZMWs.", category: "advanced"} peekGuess: {description: "Try to infer the used barcodes subset, by peeking at the first 50,000 ZMWs.", category: "advanced"}
logLevel: {description: "Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).", category: "advanced"} logLevel: {description: "Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).", category: "advanced"}
inputBamFile: {description: "BAM input file.", category: "required"} inputBamFile: {description: "Bam input file.", category: "required"}
barcodeFile: {description: "Barcode/primer fasta file.", category: "required"} barcodeFile: {description: "Barcode/primer fasta file.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"} cores: {description: "The number of cores to be used.", category: "advanced"}
...@@ -148,13 +148,13 @@ task Lima { ...@@ -148,13 +148,13 @@ task Lima {
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"} 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"}
# outputs # outputs
outputFLfile: {description: "Demultiplexed reads output file(s)."} limaBam: {description: "Demultiplexed reads output file(s)."}
outputFLindexFile: {description: "Index of demultiplexed reads output file(s)."} limaBamIndex: {description: "Index of demultiplexed reads output file(s)."}
outputFLxmlFile: {description: "XML file of the subreadset(s)."} limaXml: {description: "Xml file of the subreadset(s)."}
outputSTDERRfile: {description: "Lima STDERR log file."} limaStderr: {description: "Lima stderr log file."}
outputJSONfile: {description: "Lima JSON file."} limaJson: {description: "Lima json file."}
outputCountsFile: {description: "Lima counts file."} limaCounts: {description: "Lima counts file."}
outputReportFile: {description: "Lima report file."} limaReport: {description: "Lima report file."}
outputSummaryFile: {description: "Lima summary file."} limaSummary: {description: "Lima summary file."}
} }
} }
talon.wdl
+ 45
− 45
View file @ c248c5bb
...@@ -48,7 +48,7 @@ task CreateAbundanceFileFromDatabase { ...@@ -48,7 +48,7 @@ task CreateAbundanceFileFromDatabase {
} }
output { output {
File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv" File abundanceFile = outputPrefix + "_talon_abundance.tsv"
} }
runtime { runtime {
...@@ -59,7 +59,7 @@ task CreateAbundanceFileFromDatabase { ...@@ -59,7 +59,7 @@ task CreateAbundanceFileFromDatabase {
parameter_meta { parameter_meta {
# inputs # inputs
databaseFile: {description: "TALON database.", category: "required"} databaseFile: {description: "Talon database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"} annotationVersion: {description: "Which annotation version to use.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"} genomeBuild: {description: "Genome build to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
...@@ -70,7 +70,7 @@ task CreateAbundanceFileFromDatabase { ...@@ -70,7 +70,7 @@ task CreateAbundanceFileFromDatabase {
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"} 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"}
# outputs # outputs
outputAbundanceFile: {description: "Abundance for each transcript in the TALON database across datasets."} abundanceFile: {description: "Abundance for each transcript in the talon database across datasets."}
} }
} }
...@@ -105,7 +105,7 @@ task CreateGtfFromDatabase { ...@@ -105,7 +105,7 @@ task CreateGtfFromDatabase {
} }
output { output {
File outputGTFfile = outputPrefix + "_talon.gtf" File gtfFile = outputPrefix + "_talon.gtf"
} }
runtime { runtime {
...@@ -116,7 +116,7 @@ task CreateGtfFromDatabase { ...@@ -116,7 +116,7 @@ task CreateGtfFromDatabase {
parameter_meta { parameter_meta {
# inputs # inputs
databaseFile: {description: "TALON database.", category: "required"} databaseFile: {description: "Talon database.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"} genomeBuild: {description: "Genome build to use.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"} annotationVersion: {description: "Which annotation version to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
...@@ -128,7 +128,7 @@ task CreateGtfFromDatabase { ...@@ -128,7 +128,7 @@ task CreateGtfFromDatabase {
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"} 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"}
# outputs # outputs
outputGTFfile: {description: "The genes, transcripts, and exons stored a TALON database in GTF format."} gtfFile: {description: "The genes, transcripts, and exons stored a talon database in gtf format."}
} }
} }
...@@ -164,7 +164,7 @@ task FilterTalonTranscripts { ...@@ -164,7 +164,7 @@ task FilterTalonTranscripts {
} }
output { output {
File outputTranscriptWhitelist = outputPrefix + "_whitelist.csv" File transcriptWhitelist = outputPrefix + "_whitelist.csv"
} }
runtime { runtime {
...@@ -175,11 +175,11 @@ task FilterTalonTranscripts { ...@@ -175,11 +175,11 @@ task FilterTalonTranscripts {
parameter_meta { parameter_meta {
# inputs # inputs
databaseFile: {description: "TALON database.", category: "required"} databaseFile: {description: "Talon database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"} annotationVersion: {description: "Which annotation version to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
maxFracA: {description: "Maximum fraction of As to allow in the window located immediately after any read assigned to a novel transcript.", category: "advanced"} maxFracA: {description: "Maximum fraction of As to allow in the window located immediately after any read assigned to a novel transcript.", category: "advanced"}
minCount: {description: "Number of minimum occurrences required for a novel transcript PER dataset.", category: "advanced"} minCount: {description: "Number of minimum occurrences required for a novel transcript per dataset.", category: "advanced"}
allowGenomic: {description: "If this option is set, transcripts from the Genomic novelty category will be permitted in the output.", category: "advanced"} allowGenomic: {description: "If this option is set, transcripts from the Genomic novelty category will be permitted in the output.", category: "advanced"}
datasetsFile: {description: "Datasets to include.", category: "advanced"} datasetsFile: {description: "Datasets to include.", category: "advanced"}
minDatasets: {description: "Minimum number of datasets novel transcripts must be found in.", category: "advanced"} minDatasets: {description: "Minimum number of datasets novel transcripts must be found in.", category: "advanced"}
...@@ -188,7 +188,7 @@ task FilterTalonTranscripts { ...@@ -188,7 +188,7 @@ task FilterTalonTranscripts {
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"} 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"}
# outputs # outputs
outputTranscriptWhitelist: {description: "A transcript whitelist produced from the TALON database."} transcriptWhitelist: {description: "Transcript whitelist produced from the talon database."}
} }
} }
...@@ -216,7 +216,7 @@ task GetReadAnnotations { ...@@ -216,7 +216,7 @@ task GetReadAnnotations {
} }
output { output {
File outputAnnotation = outputPrefix + "_talon_read_annot.tsv" File readAnnotations = outputPrefix + "_talon_read_annot.tsv"
} }
runtime { runtime {
...@@ -227,7 +227,7 @@ task GetReadAnnotations { ...@@ -227,7 +227,7 @@ task GetReadAnnotations {
parameter_meta { parameter_meta {
# inputs # inputs
databaseFile: { description: "TALON database.", category: "required"} databaseFile: { description: "Talon database.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"} genomeBuild: {description: "Genome build to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"} datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
...@@ -236,7 +236,7 @@ task GetReadAnnotations { ...@@ -236,7 +236,7 @@ task GetReadAnnotations {
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"} 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"}
# outputs # outputs
outputAnnotation: {description: "Read-specific annotation information from a TALON database."} readAnnotations: {description: "Read-specific annotation information from a talon database."}
} }
} }
...@@ -266,7 +266,7 @@ task GetSpliceJunctions { ...@@ -266,7 +266,7 @@ task GetSpliceJunctions {
} }
output { output {
File outputSJfile = outputPrefix + "_" + runMode + "s.tsv" File spliceJunctions = outputPrefix + "_" + runMode + "s.tsv"
} }
runtime { runtime {
...@@ -277,9 +277,9 @@ task GetSpliceJunctions { ...@@ -277,9 +277,9 @@ task GetSpliceJunctions {
parameter_meta { parameter_meta {
# inputs # inputs
SJinformationFile: {description: "TALON GTF file or database from which to extract exons/introns.", category: "required"} SJinformationFile: {description: "Talon gtf file or database from which to extract exons/introns.", category: "required"}
inputFileType: {description: "The file type of SJinformationFile.", category: "common"} inputFileType: {description: "The file type of SJinformationFile.", category: "common"}
referenceGTF: {description: "GTF reference file (ie GENCODE).", category: "required"} referenceGTF: {description: "Gtf reference file (ie gencode).", category: "required"}
runMode: {description: "Determines whether to include introns or exons in the output.", category: "common"} runMode: {description: "Determines whether to include introns or exons in the output.", category: "common"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"} memory: {description: "The amount of memory available to the job.", category: "advanced"}
...@@ -287,7 +287,7 @@ task GetSpliceJunctions { ...@@ -287,7 +287,7 @@ task GetSpliceJunctions {
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"} 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"}
# outputs # outputs
outputSJfile: {description: "File containing locations, novelty and transcript assignments of exons/introns."} spliceJunctions: {description: "File containing locations, novelty and transcript assignments of exons/introns."}
} }
} }
...@@ -322,7 +322,7 @@ task InitializeTalonDatabase { ...@@ -322,7 +322,7 @@ task InitializeTalonDatabase {
} }
output { output {
File outputDatabase = outputPrefix + ".db" File database = outputPrefix + ".db"
} }
runtime { runtime {
...@@ -333,11 +333,11 @@ task InitializeTalonDatabase { ...@@ -333,11 +333,11 @@ task InitializeTalonDatabase {
parameter_meta { parameter_meta {
# inputs # inputs
GTFfile: {description: "GTF annotation containing genes, transcripts, and edges.", category: "required"} GTFfile: {description: "Gtf annotation containing genes, transcripts, and edges.", category: "required"}
genomeBuild: {description: "Name of genome build that the GTF file is based on (ie hg38).", category: "required"} genomeBuild: {description: "Name of genome build that the gtf file is based on (ie hg38).", category: "required"}
annotationVersion: {description: "Name of supplied annotation (will be used to label data).", category: "required"} annotationVersion: {description: "Name of supplied annotation (will be used to label data).", category: "required"}
minimumLength: { description: "Minimum required transcript length.", category: "common"} minimumLength: { description: "Minimum required transcript length.", category: "common"}
novelIDprefix: {description: "Prefix for naming novel discoveries in eventual TALON runs.", category: "common"} novelIDprefix: {description: "Prefix for naming novel discoveries in eventual talon runs.", category: "common"}
cutoff5p: { description: "Maximum allowable distance (bp) at the 5' end during annotation.", category: "advanced"} cutoff5p: { description: "Maximum allowable distance (bp) at the 5' end during annotation.", category: "advanced"}
cutoff3p: {description: "Maximum allowable distance (bp) at the 3' end during annotation.", category: "advanced"} cutoff3p: {description: "Maximum allowable distance (bp) at the 3' end during annotation.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
...@@ -346,7 +346,7 @@ task InitializeTalonDatabase { ...@@ -346,7 +346,7 @@ task InitializeTalonDatabase {
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"} 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"}
# outputs # outputs
outputDatabase: {description: "TALON database."} database: {description: "Talon database."}
} }
} }
...@@ -379,8 +379,8 @@ task LabelReads { ...@@ -379,8 +379,8 @@ task LabelReads {
} }
output { output {
File outputLabeledSAM = outputPrefix + "_labeled.sam" File labeledSam = outputPrefix + "_labeled.sam"
File outputReadLabels = outputPrefix + "_read_labels.tsv" File readLabels = outputPrefix + "_read_labels.tsv"
} }
runtime { runtime {
...@@ -392,7 +392,7 @@ task LabelReads { ...@@ -392,7 +392,7 @@ task LabelReads {
parameter_meta { parameter_meta {
# inputs # inputs
SAMfile: {description: "SAM file of transcripts.", category: "required"} SAMfile: {description: "Sam file of transcripts.", category: "required"}
referenceGenome: {description: "Reference genome fasta file.", category: "required"} referenceGenome: {description: "Reference genome fasta file.", category: "required"}
fracaRangeSize: {description: "Size of post-transcript interval to compute fraction.", category: "common"} fracaRangeSize: {description: "Size of post-transcript interval to compute fraction.", category: "common"}
tmpDir: {description: "Path to directory for tmp files.", category: "advanced"} tmpDir: {description: "Path to directory for tmp files.", category: "advanced"}
...@@ -404,8 +404,8 @@ task LabelReads { ...@@ -404,8 +404,8 @@ task LabelReads {
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"} 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"}
# outputs # outputs
outputLabeledSAM: {description: "SAM file with labeled transcripts."} labeledSam: {description: "Sam file with labeled transcripts."}
outputReadLabels: {description: "Tabular file with fraction description per read."} readLabels: {description: "Tabular file with fraction description per read."}
} }
} }
...@@ -425,7 +425,7 @@ task ReformatGtf { ...@@ -425,7 +425,7 @@ task ReformatGtf {
} }
output { output {
File outputReformattedGTF = GTFfile File reformattedGtf = GTFfile
} }
runtime { runtime {
...@@ -436,13 +436,13 @@ task ReformatGtf { ...@@ -436,13 +436,13 @@ task ReformatGtf {
parameter_meta { parameter_meta {
# inputs # inputs
GTFfile: {description: "GTF annotation containing genes, transcripts, and edges.", category: "required"} GTFfile: {description: "Gtf annotation containing genes, transcripts, and edges.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"} memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"} 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"}
# outputs # outputs
outputReformattedGTF: {description: "Reformatted GTF file."} reformattedGtf: {description: "Reformatted gtf file."}
} }
} }
...@@ -470,7 +470,7 @@ task SummarizeDatasets { ...@@ -470,7 +470,7 @@ task SummarizeDatasets {
} }
output { output {
File outputSummaryFile = outputPrefix + "_talon_summary.tsv" File summaryFile = outputPrefix + "_talon_summary.tsv"
} }
runtime { runtime {
...@@ -481,7 +481,7 @@ task SummarizeDatasets { ...@@ -481,7 +481,7 @@ task SummarizeDatasets {
parameter_meta { parameter_meta {
# inputs # inputs
databaseFile: {description: "TALON database.", category: "required"} databaseFile: {description: "Talon database.", category: "required"}
setVerbose: {description: "Print out the counts in terminal.", category: "advanced"} setVerbose: {description: "Print out the counts in terminal.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetGroupsCSV: {description: "File of comma-delimited dataset groups to process together.", category: "advanced"} datasetGroupsCSV: {description: "File of comma-delimited dataset groups to process together.", category: "advanced"}
...@@ -490,7 +490,7 @@ task SummarizeDatasets { ...@@ -490,7 +490,7 @@ task SummarizeDatasets {
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"} 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"}
# outputs # outputs
outputSummaryFile: {description: "Tab-delimited file of gene and transcript counts for each dataset."} summaryFile: {description: "Tab-delimited file of gene and transcript counts for each dataset."}
} }
} }
...@@ -534,10 +534,10 @@ task Talon { ...@@ -534,10 +534,10 @@ task Talon {
>>> >>>
output { output {
File outputUpdatedDatabase = databaseFile File updatedDatabase = databaseFile
File outputLog = outputPrefix + "/run_QC.log" File talonLog = outputPrefix + "/run_QC.log"
File outputAnnot = outputPrefix + "/run_talon_read_annot.tsv" File talonAnnotation = outputPrefix + "/run_talon_read_annot.tsv"
File outputConfigFile = outputPrefix + "/talonConfigFile.csv" File talonConfigFile = outputPrefix + "/talonConfigFile.csv"
} }
runtime { runtime {
...@@ -549,13 +549,13 @@ task Talon { ...@@ -549,13 +549,13 @@ task Talon {
parameter_meta { parameter_meta {
# inputs # inputs
SAMfiles: {description: "Input SAM files.", category: "required"} SAMfiles: {description: "Input sam files.", category: "required"}
organism: {description: "The name of the organism from which the samples originated.", category: "required"} organism: {description: "The name of the organism from which the samples originated.", category: "required"}
sequencingPlatform: {description: "The sequencing platform used to generate long reads.", category: "required"} sequencingPlatform: {description: "The sequencing platform used to generate long reads.", category: "required"}
databaseFile: {description: "TALON database. Created using initialize_talon_database.py.", category: "required"} databaseFile: {description: "Talon database. Created using initialize_talon_database.py.", category: "required"}
genomeBuild: {description: "Genome build (i.e. hg38) to use.", category: "required"} genomeBuild: {description: "Genome build (i.e. hg38) to use.", category: "required"}
minimumCoverage: {description: "Minimum alignment coverage in order to use a SAM entry.", category: "common"} minimumCoverage: {description: "Minimum alignment coverage in order to use a sam entry.", category: "common"}
minimumIdentity: {description: "Minimum alignment identity in order to use a SAM entry.", category: "common" } minimumIdentity: {description: "Minimum alignment identity in order to use a sam entry.", category: "common" }
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"} outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
threads: {description: "The number of threads to be used.", category: "advanced"} threads: {description: "The number of threads to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"} memory: {description: "The amount of memory available to the job.", category: "advanced"}
...@@ -563,9 +563,9 @@ task Talon { ...@@ -563,9 +563,9 @@ task Talon {
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"} 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"}
# outputs # outputs
outputUpdatedDatabase: {description: "Updated TALON database."} updatedDatabase: {description: "Updated talon database."}
outputLog: {description: "Log file from TALON run."} talonLog: {description: "Log file from talon run."}
outputAnnot: {description: "Read annotation file from TALON run."} talonAnnotation: {description: "Read annotation file from talon run."}
outputConfigFile: {description: "The TALON configuration file."} talonConfigFile: {description: "The talon configuration file."}
} }
} }
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