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Pipeline
Inputs
Required inputs
Pipeline.annotationGTF
File — Default: None
GTF annotation containing genes, transcripts, and edges.
Pipeline.annotationVersion
String — Default: None
Name of supplied annotation (will be used to label data).
Pipeline.dockerImagesFile
File — Default: None
The docker image used for this workflow. Changing this may result in errors which the developers may choose not to address.
Pipeline.executeSampleWorkflow.presetOption
String — Default: None
This option applies multiple options at the same time in minimap2.
Pipeline.genomeBuild
String — Default: None
Genome build (i.e. hg38) to use.
Pipeline.organismName
String — Default: None
The name of the organism from which the data was collected.
Pipeline.pipelineRunName
String — Default: None
A name describing the pipeline run.
Pipeline.referenceGenome
File — Default: None
Reference genome fasta file.
Pipeline.sampleConfigFile
File — Default: None
Samplesheet describing input fasta/fastq files.
Pipeline.sequencingPlatform
String — Default: None
The sequencing machine used to generate the data.
Other common inputs
Pipeline.createDatabase.minimumLength
Int — Default: 300
Minimum required transcript length.
Pipeline.executeSampleWorkflow.executeTranscriptClean.bufferSize
Int — Default: 100
Number of lines to output to file at once by each thread during run.
Pipeline.executeSampleWorkflow.executeTranscriptClean.correctIndels
Boolean — Default: true
Set this to make TranscriptClean correct indels.
Pipeline.executeSampleWorkflow.executeTranscriptClean.correctMismatches
Boolean — Default: true
Set this to make TranscriptClean correct mismatches.
Pipeline.executeSampleWorkflow.executeTranscriptClean.correctSJs
Boolean — Default: true
Set this to make TranscriptClean correct splice junctions.
Pipeline.executeSampleWorkflow.executeTranscriptClean.deleteTmp
Boolean — Default: true
The temporary directory generated by TranscriptClean will be removed.
Pipeline.executeSampleWorkflow.howToFindGTAG
String? — Default: None
How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG.
Pipeline.executeSampleWorkflow.variantVCF
File? — Default: None
VCF formatted file of variants.
Pipeline.executeTalon.minimumCoverage
Float — Default: 0.9
Minimum alignment coverage in order to use a SAM entry.
Pipeline.executeTalon.minimumIdentity
Int — Default: 0
Minimum alignment identity in order to use a SAM entry.
Pipeline.novelIDprefix
String — Default: "TALON"
Prefix for naming novel discoveries in eventual TALON runs.
Pipeline.outputDirectory
String — Default: "."
The directory to which the outputs will be written.
Pipeline.runTranscriptClean
Boolean — Default: true
Option to run TranscriptClean after Minimap2 alignment.
Advanced inputs
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Pipeline.convertDockerImagesFile.dockerImage
String — Default: "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
Pipeline.convertSampleConfig.checkFileMd5sums
Boolean — Default: false
Whether or not the MD5 sums of the files mentioned in the samplesheet should be checked.
Pipeline.convertSampleConfig.old
Boolean — Default: false
Whether or not the old samplesheet format should be used.
Pipeline.convertSampleConfig.skipFileCheck
Boolean — Default: true
Whether or not the existance of the files mentioned in the samplesheet should be checked.
Pipeline.createAbundanceFile.datasetsFile
File? — Default: None
A file indicating which datasets should be included.
Pipeline.createAbundanceFile.memory
String — Default: "4G"
The amount of memory available to the job.
Pipeline.createAbundanceFile.whitelistFile
File? — Default: None
Whitelist file of transcripts to include in the output.
Pipeline.createDatabase.cutoff3p
Int — Default: 300
Maximum allowable distance (bp) at the 3' end during annotation.
Pipeline.createDatabase.cutoff5p
Int — Default: 500
Maximum allowable distance (bp) at the 5' end during annotation.
Pipeline.createDatabase.memory
String — Default: "10G"
The amount of memory available to the job.
Pipeline.createSJsfile.memory
String — Default: "8G"
The amount of memory available to the job.
Pipeline.createSJsfile.minIntronSize
Int — Default: 21
Minimum size of intron to consider a junction.
Pipeline.createSummaryFile.datasetGroupsCSV
File? — Default: None
File of comma-delimited dataset groups to process together.
Pipeline.createSummaryFile.memory
String — Default: "4G"
The amount of memory available to the job.
Pipeline.createSummaryFile.setVerbose
Boolean — Default: false
Print out the counts in terminal.
Pipeline.executeSampleWorkflow.executeMinimap2.cores
Int — Default: 4
The number of cores to be used.
Pipeline.executeSampleWorkflow.executeMinimap2.kmerSize
Int — Default: 15
K-mer size (no larger than 28).
Pipeline.executeSampleWorkflow.executeMinimap2.matchingScore
Int? — Default: None
Matching score.
Pipeline.executeSampleWorkflow.executeMinimap2.maxFragmentLength
Int? — Default: None
Max fragment length (effective with -xsr or in the fragment mode).
Pipeline.executeSampleWorkflow.executeMinimap2.maxIntronLength
Int? — Default: None
Max intron length (effective with -xsplice; changing -r).
Pipeline.executeSampleWorkflow.executeMinimap2.memory
String — Default: "30G"
The amount of memory available to the job.
Pipeline.executeSampleWorkflow.executeMinimap2.mismatchPenalty
Int? — Default: None
Mismatch penalty.
Pipeline.executeSampleWorkflow.executeMinimap2.retainMaxSecondaryAlignments
Int? — Default: None
Retain at most INT secondary alignments.
Pipeline.executeSampleWorkflow.executeMinimap2.secondaryAlignment
Boolean — Default: false
Whether to output secondary alignments.
Pipeline.executeSampleWorkflow.executeMinimap2.skipSelfAndDualMappings
Boolean — Default: false
Skip self and dual mappings (for the all-vs-all mode).
Pipeline.executeSampleWorkflow.executeTranscriptClean.canonOnly
Boolean — Default: false
Only output canonical transcripts and transcript containing annotated noncanonical junctions.
Pipeline.executeSampleWorkflow.executeTranscriptClean.cores
Int — Default: 1
The number of cores to be used.
Pipeline.executeSampleWorkflow.executeTranscriptClean.dryRun
Boolean — Default: false
TranscriptClean will read in the data but don't do any correction.
Pipeline.executeSampleWorkflow.executeTranscriptClean.maxLenIndel
Int — Default: 5
Maximum size indel to correct.
Pipeline.executeSampleWorkflow.executeTranscriptClean.maxSJoffset
Int — Default: 5
Maximum distance from annotated splice junction to correct.
Pipeline.executeSampleWorkflow.executeTranscriptClean.memory
String — Default: "25G"
The amount of memory available to the job.
Pipeline.executeTalon.cores
Int — Default: 4
The number of cores to be used.
Pipeline.executeTalon.memory
String — Default: "25G"
The amount of memory available to the job.
Pipeline.spliceJunctionsFile
File? — Default: None
A pre-generated splice junction annotation file.
Pipeline.talonDatabase
File? — Default: None
A pre-generated TALON database file.
Generated using WDL AID (0.1.1)