diff --git a/CHANGELOG.md b/CHANGELOG.md
index 394eb61f28e05b68cf2bd3b94db21b904b5e4f84..7d5652fa9dd1846dfa6646d246fdcf9766bf95d0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,53 +11,55 @@ that users understand how the changes affect the new version.
version 2.1.0-dev
---------------------------
-+ Updated TALON to version 4.4
++ Updated parameter_meta sections for Minimap2 and TranscriptClean to wdl-aid format.
++ Updated cores variable for TALON, the default is now 4.
++ Updated TALON to version 4.4.
+ Added parameter_meta sections to the following tools:
+ htseq
+ cutadapt
+ collect-columns
+ stringtie
+ fastqc
-+ Updated star default image to 2.7.3a
++ Updated star default image to 2.7.3a.
+ Hisat2 now indexes the resulting BAM file.
-+ Samtools index now also works without setting a path for the output
-+ Bugfix: Biowdl-input-converter now makes sure the output directory exists
++ Samtools index now also works without setting a path for the output.
++ Bugfix: Biowdl-input-converter now makes sure the output directory exists.
version 2.0.0
---------------------------
-+ TranscriptClean: Update TranscriptClean to version 2.0.2
++ TranscriptClean: Update TranscriptClean to version 2.0.2.
+ Memory runtime attributes are now Strings indicating total memory, as opposed to Ints indicating memory per core.
+ Memory inputs for most tasks are now Strings, remaining Int memory inputs are renamed to "memoryGb".
+ Use the biowdl-input-converter container for JsonToYaml, to reduce the amount of containers needed.
+ Add biowdl-input-converter and remove SampleConfigToSampleReadgroupLists which it replaces.
-+ GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0
-+ Minimap2: Add -k option to minimap2 mapping
-+ Added bwakit task
-+ Minimap2: Add the option for --MD tag
-+ TALON: Update average memory needs for main TALON process
++ GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0 .
++ Minimap2: Add -k option to minimap2 mapping.
++ Added bwakit task.
++ Minimap2: Add the option for --MD tag.
++ TALON: Update average memory needs for main TALON process.
version 1.0.0
---------------------------
-+ Common: Add "SampleConfigToSampleReadgroupLists" task
-+ MultiQC: the "interactive" input is now set to true by default
++ Common: Add "SampleConfigToSampleReadgroupLists" task.
++ MultiQC: the "interactive" input is now set to true by default.
+ Removed deprecated tasks:
+ bioconda.installPrefix
+ mergecounts.MergeCounts
-+ GATK.BaseRecalibrator: "knownIndelsSitesVCFs" and "knownIndelsSitesVCFIndexes" are no longer optional, but now have a default of "[]"
-+ Removed BWA index task
-+ Removed unused "picardJar" input from bwa.wdl
-+ All inputs to bedtools Sort are now reflected in the generated command
-+ TranscriptClean: Update TranscriptClean container to version 1.0.8
-+ Removed "pipefail" from command sections TALON and TranscriptClean
-+ Add WDL task for Minimap2
-+ Add WDL task for TALON
-+ Add WDL task for TranscriptClean
-+ Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir
-+ Cutadapt: simplify interface
-+ Bigger memory multiplier in mutect to take in account bigger vmem usage
-+ Cutadapt: Remove default adapter
++ GATK.BaseRecalibrator: "knownIndelsSitesVCFs" and "knownIndelsSitesVCFIndexes" are no longer optional, but now have a default of "[]".
++ Removed BWA index task.
++ Removed unused "picardJar" input from bwa.wdl.
++ All inputs to bedtools Sort are now reflected in the generated command.
++ TranscriptClean: Update TranscriptClean container to version 1.0.8.
++ Removed "pipefail" from command sections TALON and TranscriptClean.
++ Add WDL task for Minimap2.
++ Add WDL task for TALON.
++ Add WDL task for TranscriptClean.
++ Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir.
++ Cutadapt: simplify interface.
++ Bigger memory multiplier in mutect to take in account bigger vmem usage.
++ Cutadapt: Remove default adapter.
+ Fastqsplitter: use version 1.1.
-+ Picard: Use version 2.20.5 of the biocontainer as this includes the R dependency
++ Picard: Use version 2.20.5 of the biocontainer as this includes the R dependency.
+ Common: Update dockerTag to dockerImage.
+ GATK: Add CombineVariants task that allows, e.g., to merge VCFs from different callers.
+ Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).
diff --git a/minimap2.wdl b/minimap2.wdl
index 6ff8cf3eaca431098e6234d6bbbd4f7ae9d0670c..c29f3314124d5120dcf2587967415d0fad576194 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 skipSelfAndDualMappings = false
+ Boolean outputSAM = false
+ String outputPrefix
+ Boolean addMDtagToSAM = false
+ Boolean secondaryAlignment = false
+ File referenceFile
+ File queryFile
- Int? maxFragmentLength
Int? maxIntronLength
- Boolean? skipSelfAndDualMappings
+ Int? maxFragmentLength
Int? retainMaxSecondaryAlignments
Int? matchingScore
Int? mismatchPenalty
String? howToFindGTAG
- Boolean? secondaryAlignment
- Boolean? addMDtagToSAM
Int cores = 4
String memory = "30G"
@@ -99,19 +119,19 @@ task Mapping {
mkdir -p $(dirname ~{outputPrefix})
minimap2 \
~{"-x " + presetOption} \
+ ~{"-k " + kmerSize} \
+ ~{true="-X" false="" skipSelfAndDualMappings} \
~{true="-a" false="" outputSAM} \
+ ~{"-o " + outputPrefix} \
+ ~{true="--MD" false="" addMDtagToSAM} \
+ --secondary=~{true="yes" false="no" secondaryAlignment} \
+ ~{"-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} \
~{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/scripts b/scripts
index e00dc247dac8f4aa91a77d6d307f928cc8449527..6eaa313f172f3efb9e62f2140b8d7fb34da6bd9a 160000
--- a/scripts
+++ b/scripts
@@ -1 +1 @@
-Subproject commit e00dc247dac8f4aa91a77d6d307f928cc8449527
+Subproject commit 6eaa313f172f3efb9e62f2140b8d7fb34da6bd9a
diff --git a/talon.wdl b/talon.wdl
index 5518ea51a484e4a22b38adee63d65a0076791226..9d3b5304fb5bc0bf665e289fce6aca86a7c85220 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -456,7 +456,7 @@ task Talon {
String configFileName = basename(configFile)
String SAMfileName = basename(SAMfile)
- Int cores = 1
+ Int cores = 4
String memory = "20G"
String dockerImage = "biocontainers/talon:v4.4_cv1"
}
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index f0053b25e9cb73f780180ca9a0090a4845bd9634..df187fd2a2a7313d1f718895e399de4762e0a1cc 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"
+ }
}
}