diff --git a/CHANGELOG.md b/CHANGELOG.md
index 22e6c56fda38058a6b841fa30f8722166f27a2ff..9796c4843eb8118ef1f058b05d71db64a0454085 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
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.
+ Removed the redundant format flag from the htseq interface. This is
autodetected in newer versions of htseq.
diff --git a/ccs.wdl b/ccs.wdl
index 1762ac75decc526370ba83d46db018a9168c5da0..60e43711ed88f587b7cc5ca9877791ceb683b4c6 100644
--- a/ccs.wdl
+++ b/ccs.wdl
@@ -55,10 +55,10 @@ task CCS {
}
output {
- File outputCCSfile = outputPrefix + ".ccs.bam"
- File outputCCSindexFile = outputPrefix + ".ccs.bam.pbi"
- File outputReportFile = outputPrefix + ".ccs.report.txt"
- File outputSTDERRfile = outputPrefix + ".ccs.stderr.log"
+ File ccsBam = outputPrefix + ".ccs.bam"
+ File ccsBamIndex = outputPrefix + ".ccs.bam.pbi"
+ File ccsReport = outputPrefix + ".ccs.report.txt"
+ File ccsStderr = outputPrefix + ".ccs.stderr.log"
}
runtime {
@@ -70,7 +70,7 @@ task CCS {
parameter_meta {
# 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"}
maxLength: {description: "Maximum draft length before polishing.", category: "advanced"}
byStrand: {description: "Generate a consensus for each strand.", category: "advanced"}
@@ -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"}
# outputs
- outputCCSfile: {description: "Consensus reads output file."}
- outputCCSindexFile: {description: "Index of consensus reads output file."}
- outputReportFile: {description: "CCS results report file."}
- outputSTDERRfile: {description: "CCS STDERR log file."}
+ ccsBam: {description: "Consensus reads output file."}
+ ccsBamIndex: {description: "Index of consensus reads output file."}
+ ccsReport: {description: "Ccs results report file."}
+ ccsStderr: {description: "Ccs STDERR log file."}
}
}
diff --git a/centrifuge.wdl b/centrifuge.wdl
index f2b26043de9becf264f1d136e2d5a39a1429c723..e1cddcadedd9e5c6e110684cb0c702cb0e77b2e2 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -59,7 +59,7 @@ task Build {
}
output {
- Array[File] outputIndex = glob(outputPrefix + "/" + indexBasename + "*.cf")
+ Array[File] index = glob(outputPrefix + "/" + indexBasename + "*.cf")
}
runtime {
@@ -75,7 +75,7 @@ task Build {
conversionTable: {description: "List of UIDs (unique ID) and corresponding taxonomic IDs.", category: "required"}
taxonomyTree: {description: "Taxonomic tree (e.g. nodes.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"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
offrate: {description: "The number of rows marked by the indexer.", category: "common"}
@@ -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"}
# outputs
- outputIndex: {description: "Generated Centrifuge index."}
+ index: {description: "Generated centrifuge index."}
}
}
@@ -142,9 +142,9 @@ task Classify {
>>>
output {
- File outputMetrics = outputPrefix + "_alignment_metrics.tsv"
- File outputClassification = outputPrefix + "_classification.tsv"
- File outputReport = outputPrefix + "_output_report.tsv"
+ File metrics = outputPrefix + "_alignment_metrics.tsv"
+ File classification = outputPrefix + "_classification.tsv"
+ File report = outputPrefix + "_output_report.tsv"
}
runtime {
@@ -156,7 +156,7 @@ task Classify {
parameter_meta {
# inputs
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"}
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"}
@@ -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"}
# outputs
- outputMetrics: {description: "File with Centrifuge metrics."}
- outputClassification: {description: "File with the classification results."}
- outputReport: {description: "File with a classification summary."}
+ metrics: {description: "File with centrifuge metrics."}
+ classification: {description: "File with the classification results."}
+ report: {description: "File with a classification summary."}
}
}
@@ -209,7 +209,7 @@ task Inspect {
>>>
output {
- File outputInspect = outputPrefix + "/" + printOption
+ File inspectResult = outputPrefix + "/" + printOption
}
runtime {
@@ -223,13 +223,13 @@ task Inspect {
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"}
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"}
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"}
# outputs
- outputInspect: {description: "Output file according to output option."}
+ inspectResult: {description: "Output file according to output option."}
}
}
@@ -300,7 +300,7 @@ task DownloadTaxonomy {
}
}
-task Kreport {
+task KReport {
input {
File centrifugeClassification
String outputPrefix
@@ -337,7 +337,7 @@ task Kreport {
>>>
output {
- File outputKreport = outputPrefix + "_kreport.tsv"
+ File KReport = outputPrefix + "_kreport.tsv"
}
runtime {
@@ -348,10 +348,10 @@ task Kreport {
parameter_meta {
# 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"}
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"}
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"}
@@ -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"}
# outputs
- outputKreport: {description: "File with kraken style report."}
+ KReport: {description: "File with kraken style report."}
}
}
@@ -384,7 +384,7 @@ task KTimportTaxonomy {
}
output {
- File outputKronaPlot = outputPrefix + "_krona.html"
+ File kronaPlot = outputPrefix + "_krona.html"
}
runtime {
@@ -395,13 +395,13 @@ task KTimportTaxonomy {
parameter_meta {
# 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"}
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"}
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
- outputKronaPlot: {description: "Krona taxonomy plot html file."}
+ kronaPlot: {description: "Krona taxonomy plot html file."}
}
}
diff --git a/isoseq3.wdl b/isoseq3.wdl
index 9e0dfdb2f43d4ba4ea2dd1807eb152ece5a15446..f369553f6265272e96b095ca4813ecfe947f1a0c 100644
--- a/isoseq3.wdl
+++ b/isoseq3.wdl
@@ -51,12 +51,12 @@ task Refine {
}
output {
- File outputFLNCfile = outputDir + "/" + outputNamePrefix + ".bam"
- File outputFLNCindexFile = outputDir + "/" + outputNamePrefix + ".bam.pbi"
- File outputConsensusReadsetFile = outputDir + "/" + outputNamePrefix + ".consensusreadset.xml"
- File outputFilterSummaryFile = outputDir + "/" + outputNamePrefix + ".filter_summary.json"
- File outputReportFile = outputDir + "/" + outputNamePrefix + ".report.csv"
- File outputSTDERRfile = outputDir + "/" + outputNamePrefix + ".stderr.log"
+ File refineBam = outputDir + "/" + outputNamePrefix + ".bam"
+ File refineBamIndex = outputDir + "/" + outputNamePrefix + ".bam.pbi"
+ File refineConsensusReadset = outputDir + "/" + outputNamePrefix + ".consensusreadset.xml"
+ File refineFilterSummary = outputDir + "/" + outputNamePrefix + ".filter_summary.json"
+ File refineReport = outputDir + "/" + outputNamePrefix + ".report.csv"
+ File refineStderr = outputDir + "/" + outputNamePrefix + ".stderr.log"
}
runtime {
@@ -69,9 +69,9 @@ task Refine {
parameter_meta {
# inputs
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"}
- inputBamFile: {description: "BAM input file.", category: "required"}
+ inputBamFile: {description: "Bam input file.", category: "required"}
primerFile: {description: "Barcode/primer fasta file.", category: "required"}
outputDir: {description: "Output directory path.", category: "required"}
outputNamePrefix: {description: "Basename of the output files.", category: "required"}
@@ -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"}
# outputs
- outputFLNCfile: {description: "Filtered reads output file."}
- outputFLNCindexFile: {description: "Index of filtered reads output file."}
- outputSTDERRfile: {description: "Refine STDERR log file."}
- outputConsensusReadsetFile: {description: "Refine consensus readset XML file."}
- outputFilterSummaryFile: {description: "Refine summary file."}
- outputReportFile: {description: "Refine report file."}
+ refineBam: {description: "Filtered reads output file."}
+ refineBamIndex: {description: "Index of filtered reads output file."}
+ refineConsensusReadset: {description: "Refine consensus readset xml file."}
+ refineFilterSummary: {description: "Refine summary file."}
+ refineReport: {description: "Refine report file."}
+ refineStderr: {description: "Refine stderr log file."}
}
}
diff --git a/lima.wdl b/lima.wdl
index ddd37da4237296c40349fa4d6b3b553924fbaadd..2e8a708502598bba6e7839e21fd0dc557ce6e56e 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -98,14 +98,14 @@ task Lima {
}
output {
- Array[File] outputFLfile = glob("*.bam")
- Array[File] outputFLindexFile = glob("*.bam.pbi")
- Array[File] outputFLxmlFile = glob("*.subreadset.xml")
- File outputSTDERRfile = outputPrefix + ".fl.stderr.log"
- File outputJSONfile = outputPrefix + ".fl.json"
- File outputCountsFile = outputPrefix + ".fl.lima.counts"
- File outputReportFile = outputPrefix + ".fl.lima.report"
- File outputSummaryFile = outputPrefix + ".fl.lima.summary"
+ Array[File] limaBam = glob("*.bam")
+ Array[File] limaBamIndex = glob("*.bam.pbi")
+ Array[File] limaXml = glob("*.subreadset.xml")
+ File limaStderr = outputPrefix + ".fl.stderr.log"
+ File limaJson = outputPrefix + ".fl.json"
+ File limaCounts = outputPrefix + ".fl.lima.counts"
+ File limaReport = outputPrefix + ".fl.lima.report"
+ File limaSummary = outputPrefix + ".fl.lima.summary"
}
runtime {
@@ -131,15 +131,15 @@ task Lima {
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"}
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"}
- splitBamNamed: {description: "Split BAM output by resolved barcode pair name.", category: "common"}
+ ccsMode: {description: "Ccs mode, use optimal alignment options.", 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"}
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"}
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"}
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"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
@@ -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"}
# outputs
- outputFLfile: {description: "Demultiplexed reads output file(s)."}
- outputFLindexFile: {description: "Index of demultiplexed reads output file(s)."}
- outputFLxmlFile: {description: "XML file of the subreadset(s)."}
- outputSTDERRfile: {description: "Lima STDERR log file."}
- outputJSONfile: {description: "Lima JSON file."}
- outputCountsFile: {description: "Lima counts file."}
- outputReportFile: {description: "Lima report file."}
- outputSummaryFile: {description: "Lima summary file."}
+ limaBam: {description: "Demultiplexed reads output file(s)."}
+ limaBamIndex: {description: "Index of demultiplexed reads output file(s)."}
+ limaXml: {description: "Xml file of the subreadset(s)."}
+ limaStderr: {description: "Lima stderr log file."}
+ limaJson: {description: "Lima json file."}
+ limaCounts: {description: "Lima counts file."}
+ limaReport: {description: "Lima report file."}
+ limaSummary: {description: "Lima summary file."}
}
}
diff --git a/talon.wdl b/talon.wdl
index a469ddbac873944a9236cd53611b8fd8b46c7981..e39a3cd2e683b660624feb71890930bb535ba650 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -48,7 +48,7 @@ task CreateAbundanceFileFromDatabase {
}
output {
- File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv"
+ File abundanceFile = outputPrefix + "_talon_abundance.tsv"
}
runtime {
@@ -59,7 +59,7 @@ task CreateAbundanceFileFromDatabase {
parameter_meta {
# inputs
- databaseFile: {description: "TALON database.", category: "required"}
+ databaseFile: {description: "Talon database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
@@ -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"}
# 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 {
}
output {
- File outputGTFfile = outputPrefix + "_talon.gtf"
+ File gtfFile = outputPrefix + "_talon.gtf"
}
runtime {
@@ -116,7 +116,7 @@ task CreateGtfFromDatabase {
parameter_meta {
# inputs
- databaseFile: {description: "TALON database.", category: "required"}
+ databaseFile: {description: "Talon database.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
@@ -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"}
# 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 {
}
output {
- File outputTranscriptWhitelist = outputPrefix + "_whitelist.csv"
+ File transcriptWhitelist = outputPrefix + "_whitelist.csv"
}
runtime {
@@ -175,11 +175,11 @@ task FilterTalonTranscripts {
parameter_meta {
# inputs
- databaseFile: {description: "TALON database.", category: "required"}
+ databaseFile: {description: "Talon database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", 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"}
- 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"}
datasetsFile: {description: "Datasets to include.", category: "advanced"}
minDatasets: {description: "Minimum number of datasets novel transcripts must be found in.", category: "advanced"}
@@ -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"}
# 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 {
}
output {
- File outputAnnotation = outputPrefix + "_talon_read_annot.tsv"
+ File readAnnotations = outputPrefix + "_talon_read_annot.tsv"
}
runtime {
@@ -227,7 +227,7 @@ task GetReadAnnotations {
parameter_meta {
# inputs
- databaseFile: { description: "TALON database.", category: "required"}
+ databaseFile: { description: "Talon database.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
@@ -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"}
# 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 {
}
output {
- File outputSJfile = outputPrefix + "_" + runMode + "s.tsv"
+ File spliceJunctions = outputPrefix + "_" + runMode + "s.tsv"
}
runtime {
@@ -277,9 +277,9 @@ task GetSpliceJunctions {
parameter_meta {
# 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"}
- 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"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
@@ -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"}
# 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 {
}
output {
- File outputDatabase = outputPrefix + ".db"
+ File database = outputPrefix + ".db"
}
runtime {
@@ -333,11 +333,11 @@ task InitializeTalonDatabase {
parameter_meta {
# inputs
- 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"}
+ 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"}
annotationVersion: {description: "Name of supplied annotation (will be used to label data).", category: "required"}
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"}
cutoff3p: {description: "Maximum allowable distance (bp) at the 3' end during annotation.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
@@ -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"}
# outputs
- outputDatabase: {description: "TALON database."}
+ database: {description: "Talon database."}
}
}
@@ -379,8 +379,8 @@ task LabelReads {
}
output {
- File outputLabeledSAM = outputPrefix + "_labeled.sam"
- File outputReadLabels = outputPrefix + "_read_labels.tsv"
+ File labeledSam = outputPrefix + "_labeled.sam"
+ File readLabels = outputPrefix + "_read_labels.tsv"
}
runtime {
@@ -392,7 +392,7 @@ task LabelReads {
parameter_meta {
# 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"}
fracaRangeSize: {description: "Size of post-transcript interval to compute fraction.", category: "common"}
tmpDir: {description: "Path to directory for tmp files.", category: "advanced"}
@@ -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"}
# outputs
- outputLabeledSAM: {description: "SAM file with labeled transcripts."}
- outputReadLabels: {description: "Tabular file with fraction description per read."}
+ labeledSam: {description: "Sam file with labeled transcripts."}
+ readLabels: {description: "Tabular file with fraction description per read."}
}
}
@@ -425,7 +425,7 @@ task ReformatGtf {
}
output {
- File outputReformattedGTF = GTFfile
+ File reformattedGtf = GTFfile
}
runtime {
@@ -436,13 +436,13 @@ task ReformatGtf {
parameter_meta {
# 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"}
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"}
# outputs
- outputReformattedGTF: {description: "Reformatted GTF file."}
+ reformattedGtf: {description: "Reformatted gtf file."}
}
}
@@ -470,7 +470,7 @@ task SummarizeDatasets {
}
output {
- File outputSummaryFile = outputPrefix + "_talon_summary.tsv"
+ File summaryFile = outputPrefix + "_talon_summary.tsv"
}
runtime {
@@ -481,7 +481,7 @@ task SummarizeDatasets {
parameter_meta {
# inputs
- databaseFile: {description: "TALON database.", category: "required"}
+ databaseFile: {description: "Talon database.", category: "required"}
setVerbose: {description: "Print out the counts in terminal.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetGroupsCSV: {description: "File of comma-delimited dataset groups to process together.", category: "advanced"}
@@ -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"}
# 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 {
>>>
output {
- File outputUpdatedDatabase = databaseFile
- File outputLog = outputPrefix + "/run_QC.log"
- File outputAnnot = outputPrefix + "/run_talon_read_annot.tsv"
- File outputConfigFile = outputPrefix + "/talonConfigFile.csv"
+ File updatedDatabase = databaseFile
+ File talonLog = outputPrefix + "/run_QC.log"
+ File talonAnnotation = outputPrefix + "/run_talon_read_annot.tsv"
+ File talonConfigFile = outputPrefix + "/talonConfigFile.csv"
}
runtime {
@@ -549,13 +549,13 @@ task Talon {
parameter_meta {
# 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"}
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"}
- 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" }
+ 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" }
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
threads: {description: "The number of threads to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
@@ -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"}
# outputs
- outputUpdatedDatabase: {description: "Updated TALON database."}
- outputLog: {description: "Log file from TALON run."}
- outputAnnot: {description: "Read annotation file from TALON run."}
- outputConfigFile: {description: "The TALON configuration file."}
+ updatedDatabase: {description: "Updated talon database."}
+ talonLog: {description: "Log file from talon run."}
+ talonAnnotation: {description: "Read annotation file from talon run."}
+ talonConfigFile: {description: "The talon configuration file."}
}
}