diff --git a/CHANGELOG.md b/CHANGELOG.md
index 394eb61f28e05b68cf2bd3b94db21b904b5e4f84..13573295bd794e798758dba326d8b8556b73f010 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 2.1.0-dev
---------------------------
++ Updated parameter_meta sections for Minimap2 and TranscriptClean.
++ Updated cores variable for TALON.
+ Updated TALON to version 4.4
+ Added parameter_meta sections to the following tools:
+ htseq
diff --git a/minimap2.wdl b/minimap2.wdl
index 6ff8cf3eaca431098e6234d6bbbd4f7ae9d0670c..f63817c827f5eb52b7cc8d776f4ae09ffd95923d 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -22,11 +22,11 @@ version 1.0
task Indexing {
input {
- File referenceFile
- String outputPrefix
Boolean useHomopolymerCompressedKmer = false
Int kmerSize = 15
Int minimizerWindowSize = 10
+ String outputPrefix
+ File referenceFile
Int? splitIndex
@@ -42,9 +42,9 @@ task Indexing {
~{true="-H" false="" useHomopolymerCompressedKmer} \
~{"-k " + kmerSize} \
~{"-w " + minimizerWindowSize} \
- ~{"-I " + splitIndex} \
~{"-d " + outputPrefix + ".mmi"} \
~{"-t " + cores} \
+ ~{"-I " + splitIndex} \
~{referenceFile}
}
@@ -59,35 +59,55 @@ task Indexing {
}
parameter_meta {
- referenceFile: "Reference fasta file."
- outputPrefix: "Output directory path + output file prefix."
- useHomopolymerCompressedKmer: "Use homopolymer-compressed k-mer (preferrable for PacBio)."
- kmerSize: "K-mer size (no larger than 28)."
- minimizerWindowSize: "Minimizer window size."
- splitIndex: "Split index for every ~NUM input bases."
-
- outputIndexFile: "Indexed reference file."
+ useHomopolymerCompressedKmer: {
+ description: "Use homopolymer-compressed k-mer (preferrable for PacBio).",
+ category: "advanced"
+ }
+ kmerSize: {
+ description: "K-mer size (no larger than 28).",
+ category: "advanced"
+ }
+ minimizerWindowSize: {
+ description: "Minimizer window size.",
+ category: "advanced"
+ }
+ outputPrefix: {
+ description: "Output directory path + output file prefix.",
+ category: "required"
+ }
+ referenceFile: {
+ description: "Reference fasta file.",
+ category: "required"
+ }
+ splitIndex: {
+ description: "Split index for every ~NUM input bases."
+ category: "advanced"
+ }
+ outputIndexFile: {
+ description: "Indexed reference file."
+ category: "required"
+ }
}
}
task Mapping {
input {
- File queryFile
- File referenceFile
- String outputPrefix
String presetOption
- Boolean outputSAM = false
Int kmerSize = 15
+ Boolean outputSAM = false
+ String outputPrefix
+ File referenceFile
+ File queryFile
- Int? maxFragmentLength
Int? maxIntronLength
+ Int? maxFragmentLength
Boolean? skipSelfAndDualMappings
Int? retainMaxSecondaryAlignments
Int? matchingScore
Int? mismatchPenalty
String? howToFindGTAG
- Boolean? secondaryAlignment
Boolean? addMDtagToSAM
+ Boolean? secondaryAlignment
Int cores = 4
String memory = "30G"
@@ -99,19 +119,19 @@ task Mapping {
mkdir -p $(dirname ~{outputPrefix})
minimap2 \
~{"-x " + presetOption} \
+ ~{"-k " + kmerSize} \
~{true="-a" false="" outputSAM} \
+ ~{"-o " + outputPrefix} \
+ ~{"-t " + cores} \
~{"-G " + maxIntronLength} \
~{"-F " + maxFragmentLength} \
- ~{"-k " + kmerSize} \
~{true="-X" false="" skipSelfAndDualMappings} \
~{"-N " + retainMaxSecondaryAlignments} \
~{"-A " + matchingScore} \
~{"-B " + mismatchPenalty} \
~{"-u " + howToFindGTAG} \
- --secondary=~{true="yes" false="no" secondaryAlignment} \
~{true="--MD" false="" addMDtagToSAM} \
- ~{"-o " + outputPrefix} \
- ~{"-t " + cores} \
+ --secondary=~{true="yes" false="no" secondaryAlignment} \
~{referenceFile} \
~{queryFile}
}
@@ -127,22 +147,69 @@ task Mapping {
}
parameter_meta {
- queryFile: "Input fasta file."
- referenceFile: "Reference fasta file."
- outputPrefix: "Output directory path + output file prefix."
- presetOption: "This option applies multiple options at the same time."
- outputSAM: "Output in the SAM format."
- maxFragmentLength: "Max fragment length (effective with -xsr or in the fragment mode)."
- maxIntronLength: "Max intron length (effective with -xsplice; changing -r)."
- kmerSize: "K-mer size (no larger than 28)."
- skipSelfAndDualMappings: "Skip self and dual mappings (for the all-vs-all mode)."
- retainMaxSecondaryAlignments: "Retain at most INT secondary alignments."
- matchingScore: "Matching score."
- mismatchPenalty: "Mismatch penalty."
- howToFindGTAG: "How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG."
- secondaryAlignment: "Whether to output secondary alignments."
- addMDtagToSAM: "Adds a MD tag to the SAM output file."
-
- outputAlignmentFile: "Mapping and alignment between collections of DNA sequences file."
+ presetOption: {
+ description: "This option applies multiple options at the same time.",
+ category: "common"
+ }
+ kmerSize: {
+ description: "K-mer size (no larger than 28).",
+ category: "advanced"
+ }
+ outputSAM: {
+ description: "Output in the SAM format.",
+ category: "common"
+ }
+ outputPrefix: {
+ description: "Output directory path + output file prefix.",
+ category: "required"
+ }
+ maxIntronLength: {
+ description: "Max intron length (effective with -xsplice; changing -r).",
+ category: "advanced"
+ }
+ maxFragmentLength: {
+ description: "Max fragment length (effective with -xsr or in the fragment mode).",
+ category: "advanced"
+ }
+ skipSelfAndDualMappings: {
+ description: "Skip self and dual mappings (for the all-vs-all mode).",
+ category: "advanced"
+ }
+ retainMaxSecondaryAlignments: {
+ description: "Retain at most INT secondary alignments.",
+ category: "advanced"
+ }
+ matchingScore: {
+ description: "Matching score.",
+ category: "advanced"
+ }
+ mismatchPenalty: {
+ description: "Mismatch penalty.",
+ category: "advanced"
+ }
+ howToFindGTAG: {
+ description: "How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG.",
+ category: "common"
+ }
+ addMDtagToSAM: {
+ description: "Adds a MD tag to the SAM output file.",
+ category: "common"
+ }
+ secondaryAlignment: {
+ description: "Whether to output secondary alignments.",
+ category: "advanced"
+ }
+ referenceFile: {
+ description: "Reference fasta file.",
+ category: "required"
+ }
+ queryFile: {
+ description: "Input fasta file.",
+ category: "required"
+ }
+ outputAlignmentFile: {
+ description: "Mapping and alignment between collections of DNA sequences file.",
+ category: "required"
+ }
}
}
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index f0053b25e9cb73f780180ca9a0090a4845bd9634..de2c0cf5e4fa34cfb8d1be35786a7a5eeb661d6c 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -38,8 +38,8 @@ task GetSJsFromGtf {
get_SJs_from_gtf \
~{"--f=" + GTFfile} \
~{"--g=" + genomeFile} \
- ~{"--o=" + outputPrefix + ".tsv"} \
- ~{"--minIntronSize=" + minIntronSize}
+ ~{"--minIntronSize=" + minIntronSize} \
+ ~{"--o=" + outputPrefix + ".tsv"}
}
output {
@@ -53,12 +53,26 @@ task GetSJsFromGtf {
}
parameter_meta {
- GTFfile: "Input GTF file"
- genomeFile: "Reference genome"
- outputPrefix: "Output directory path + output file prefix."
- minIntronSize: "Minimum size of intron to consider a junction."
-
- outputSJsFile: "Extracted splice junctions."
+ GTFfile: {
+ description: "Input GTF file",
+ category: "required"
+ }
+ genomeFile: {
+ description: "Reference genome",
+ category: "required"
+ }
+ minIntronSize: {
+ description: "Minimum size of intron to consider a junction.",
+ category: "advanced"
+ }
+ outputPrefix: {
+ description: "Output directory path + output file prefix.",
+ category: "required"
+ }
+ outputSJsFile: {
+ description: "Extracted splice junctions.",
+ category: "required"
+ }
}
}
@@ -91,10 +105,18 @@ task GetTranscriptCleanStats {
}
parameter_meta {
- transcriptCleanSAMfile: "Output SAM file from TranscriptClean"
- outputPrefix: "Output directory path + output file prefix."
-
- outputStatsFile: "Summary stats from TranscriptClean run."
+ transcriptCleanSAMfile: {
+ description: "Output SAM file from TranscriptClean",
+ category: "required"
+ }
+ outputPrefix: {
+ description: "Output directory path + output file prefix.",
+ category: "required"
+ }
+ outputStatsFile: {
+ description: "Summary stats from TranscriptClean run."
+ category: "required"
+ }
}
}
@@ -102,9 +124,9 @@ task TranscriptClean {
input {
File SAMfile
File referenceGenome
- String outputPrefix
Int maxLenIndel = 5
Int maxSJoffset = 5
+ String outputPrefix
Boolean correctMismatches = true
Boolean correctIndels = true
Boolean correctSJs = true
@@ -112,6 +134,7 @@ task TranscriptClean {
Boolean primaryOnly = false
Boolean canonOnly = false
Int bufferSize = 100
+ Boolean deleteTmp = true
File? spliceJunctionAnnotation
File? variantFile
@@ -127,11 +150,10 @@ task TranscriptClean {
TranscriptClean \
~{"-s " + SAMfile} \
~{"-g " + referenceGenome} \
- ~{"-o " + outputPrefix} \
- ~{"-j " + spliceJunctionAnnotation} \
- ~{"-v " + variantFile} \
+ ~{"-t " + cores} \
~{"--maxLenIndel=" + maxLenIndel} \
~{"--maxSJOffset=" + maxSJoffset} \
+ ~{"-o " + outputPrefix} \
~{true="-m true" false="-m false" correctMismatches} \
~{true="-i true" false="-i false" correctIndels} \
~{true="--correctSJs=true" false="--correctSJs=false" correctSJs} \
@@ -139,7 +161,9 @@ task TranscriptClean {
~{true="--primaryOnly" false="" primaryOnly} \
~{true="--canonOnly" false="" canonOnly} \
~{"--bufferSize=" + bufferSize} \
- ~{"-t " + cores}
+ ~{true="--deleteTmp" false="" deleteTmp} \
+ ~{"-j " + spliceJunctionAnnotation} \
+ ~{"-v " + variantFile}
}
output {
@@ -156,24 +180,81 @@ task TranscriptClean {
}
parameter_meta {
- SAMfile: "Input SAM file containing transcripts to correct."
- referenceGenome: "Reference genome fasta file."
- outputPrefix: "Output directory path + output file prefix."
- spliceJunctionAnnotation: "Splice junction file."
- variantFile: "VCF formatted file of variants."
- maxLenIndel: "Maximum size indel to correct."
- maxSJoffset: "Maximum distance from annotated splice junction to correct."
- correctMismatches: "Set this to make TranscriptClean correct mismatches."
- correctIndels: "Set this to make TranscriptClean correct indels."
- correctSJs: "Set this to make TranscriptClean correct splice junctions."
- dryRun: "TranscriptClean will read in the data but don't do any correction."
- primaryOnly: "TranscriptClean will only output primary mappings of transcripts."
- canonOnly: "TranscriptClean will output only canonical transcripts and transcript containing annotated noncanonical junctions."
- bufferSize: "Number of lines to output to file at once by each thread during run."
-
- outputTranscriptCleanFasta: "Fasta file containing corrected reads."
- outputTranscriptCleanLog: "Log file of TranscriptClean run."
- outputTranscriptCleanSAM: "SAM file containing corrected aligned reads."
- outputTranscriptCleanTElog: "TE log file of TranscriptClean run."
+ SAMfile: {
+ description: "Input SAM file containing transcripts to correct.",
+ category: "required"
+ }
+ referenceGenome: {
+ description: "Reference genome fasta file.",
+ category: "required"
+ }
+ maxLenIndel: {
+ description: "Maximum size indel to correct.",
+ category: "advanced"
+ }
+ maxSJoffset: {
+ description: "Maximum distance from annotated splice junction to correct.",
+ category: "advanced"
+ }
+ outputPrefix: {
+ description: "Output directory path + output file prefix.",
+ category: "required"
+ }
+ correctMismatches: {
+ description: "Set this to make TranscriptClean correct mismatches.",
+ category: "common"
+ }
+ correctIndels: {
+ description: "Set this to make TranscriptClean correct indels.",
+ category: "common"
+ }
+ correctSJs: {
+ description: "Set this to make TranscriptClean correct splice junctions.",
+ category: "common"
+ }
+ dryRun: {
+ description: "TranscriptClean will read in the data but don't do any correction.",
+ category: "advanced"
+ }
+ primaryOnly: {
+ description: "Only output primary mappings of transcripts.",
+ category: "advanced"
+ }
+ canonOnly: {
+ description: "Only output canonical transcripts and transcript containing annotated noncanonical junctions.",
+ category: "advanced"
+ }
+ bufferSize: {
+ description: "Number of lines to output to file at once by each thread during run.",
+ category: "common"
+ }
+ deleteTmp: {
+ description: "The temporary directory generated by TranscriptClean will be removed.",
+ category: "common"
+ }
+ spliceJunctionAnnotation: {
+ description: "Splice junction file.",
+ category: "common"
+ }
+ variantFile: {
+ description: "VCF formatted file of variants.",
+ category: "common"
+ }
+ outputTranscriptCleanFasta: {
+ description: "Fasta file containing corrected reads.",
+ category: "required"
+ }
+ outputTranscriptCleanLog: {
+ description: "Log file of TranscriptClean run.",
+ category: "required"
+ }
+ outputTranscriptCleanSAM: {
+ description: "SAM file containing corrected aligned reads.",
+ category: "required"
+ }
+ outputTranscriptCleanTElog: {
+ description: "TE log file of TranscriptClean run.",
+ category: "required"
+ }
}
}