diff --git a/talon.wdl b/talon.wdl
index b5cd0d3fd8e525c7492cd6301a8f3ca199192dd5..5518ea51a484e4a22b38adee63d65a0076791226 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -23,28 +23,28 @@ version 1.0
task CreateAbundanceFileFromDatabase {
input {
File databaseFile
- String outputPrefix
- String genomeBuild
String annotationVersion
- Boolean filterTranscripts = false
+ String genomeBuild
+ String outputPrefix
- File? filterPairingsFile
+ File? whitelistFile
+ File? datasetsFile
Int cores = 1
String memory = "4G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
set -e
mkdir -p $(dirname ~{outputPrefix})
- create_abundance_file_from_database \
+ talon_abundance \
~{"--db=" + databaseFile} \
- ~{"--o=" + outputPrefix} \
- ~{"-b " + genomeBuild} \
~{"-a " + annotationVersion} \
- ~{true="--filter" false="" filterTranscripts} \
- ~{"-p " + filterPairingsFile}
+ ~{"-b " + genomeBuild} \
+ ~{"--o=" + outputPrefix} \
+ ~{"--whitelist=" + whitelistFile} \
+ ~{"-d " + datasetsFile}
}
output {
@@ -58,47 +58,68 @@ task CreateAbundanceFileFromDatabase {
}
parameter_meta {
- databaseFile: "TALON database."
- outputPrefix: "Output directory path + output file prefix."
- genomeBuild: "Genome build to use."
- annotationVersion: "Which annotation version to use."
- filterTranscripts: "The transcripts in the database will be filtered prior to GTF creation."
- filterPairingsFile: "A file indicating which datasets should be considered together."
-
- outputAbundanceFile: "Abundance for each transcript in the TALON database across datasets."
+ 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"
+ }
+ whitelistFile: {
+ description: "Whitelist file of transcripts to include in the output.",
+ category: "advanced"
+ }
+ datasetsFile: {
+ description: "A file indicating which datasets should be included.",
+ category: "advanced"
+ }
+ outputAbundanceFile: {
+ description: "Abundance for each transcript in the TALON database across datasets.",
+ category: "required"
+ }
}
}
-task CreateGtfAbundanceFromDatabase {
+task CreateGtfFromDatabase {
input {
File databaseFile
- String outputPrefix
String genomeBuild
String annotationVersion
- Boolean filterTranscripts = false
+ String outputPrefix
+ Boolean observedInDataset = false
- File? filterPairingsFile
+ File? whitelistFile
+ File? datasetFile
Int cores = 1
String memory = "4G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
set -e
mkdir -p $(dirname ~{outputPrefix})
- create_GTF_abundance_from_database \
+ talon_create_GTF \
~{"--db=" + databaseFile} \
- ~{"--o=" + outputPrefix} \
~{"-b " + genomeBuild} \
~{"-a " + annotationVersion} \
- ~{true="--filter" false="" filterTranscripts} \
- ~{"-p " + filterPairingsFile}
+ ~{"--o=" + outputPrefix} \
+ ~{"--whitelist=" + whitelistFile} \
+ ~{true="--observed" false="" observedInDataset} \
+ ~{"-d " + datasetFile}
}
output {
- File outputGTFfile = outputPrefix + "_talon_observedOnly.gtf"
- File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv"
+ File outputGTFfile = outputPrefix + "_talon.gtf"
}
runtime {
@@ -108,49 +129,66 @@ task CreateGtfAbundanceFromDatabase {
}
parameter_meta {
- databaseFile: "TALON database."
- outputPrefix: "Output directory path + output file prefix."
- genomeBuild: "Genome build to use."
- annotationVersion: "Which annotation version to use."
- filterTranscripts: "The transcripts in the database will be filtered prior to GTF creation."
- filterPairingsFile: "A file indicating which datasets should be considered together."
-
- outputGTFfile: "The genes, transcripts, and exons stored a TALON database in GTF format."
- outputAbundanceFile: "Abundance for each transcript in the TALON database across datasets."
+ 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"
+ }
+ observedInDataset: {
+ description: "The output will only include transcripts that were observed at least once.",
+ category: "advanced"
+ }
+ whitelistFile: {
+ description: "Whitelist file of transcripts to include in the output.",
+ category: "advanced"
+ }
+ datasetFile: {
+ description: "A file indicating which datasets should be included.",
+ category: "advanced"
+ }
+ outputGTFfile: {
+ description: "The genes, transcripts, and exons stored a TALON database in GTF format.",
+ category: "required"
+ }
}
}
-task CreateGtfFromDatabase {
+task FilterTalonTranscripts {
input {
File databaseFile
- String outputPrefix
- String genomeBuild
String annotationVersion
- Boolean observedInDataset = false
+ String outputPrefix
- File? whitelistFile
- File? datasetFile
+ File? pairingsFile
Int cores = 1
String memory = "4G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
set -e
mkdir -p $(dirname ~{outputPrefix})
- create_GTF_from_database \
+ talon_filter_transcripts \
~{"--db=" + databaseFile} \
- ~{"--o=" + outputPrefix} \
- ~{"-b " + genomeBuild} \
~{"-a " + annotationVersion} \
- ~{"--whitelist=" + whitelistFile} \
- ~{true="--observed" false="" observedInDataset} \
- ~{"-d " + datasetFile}
+ ~{"--o=" + outputPrefix + "_whitelist.csv"} \
+ ~{"-p " + pairingsFile}
}
output {
- File outputGTFfile = outputPrefix + "_talon.gtf"
+ File outputTranscriptWhitelist = outputPrefix + "_whitelist.csv"
}
runtime {
@@ -160,46 +198,110 @@ task CreateGtfFromDatabase {
}
parameter_meta {
- databaseFile: "TALON database."
- outputPrefix: "Output directory path + output file prefix."
- genomeBuild: "Genome build to use."
- annotationVersion: "Which annotation version to use."
- observedInDataset: "Output only includes transcripts that were observed at least once."
- whitelistFile: "Whitelist file of transcripts to include in the output."
- datasetFile: "A file indicating which datasets should be included."
+ 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"
+ }
+ pairingsFile: {
+ description: "A file indicating which datasets should be considered together.",
+ category: "advanced"
+ }
+ }
+}
+
+task GetReadAnnotations {
+ input {
+ File databaseFile
+ String genomeBuild
+ String outputPrefix
- outputGTFfile: "The genes, transcripts, and exons stored a TALON database in GTF format."
+ File? datasetFile
+
+ Int cores = 1
+ String memory = "4G"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ talon_fetch_reads \
+ ~{"--db " + databaseFile} \
+ ~{"--build " + genomeBuild} \
+ ~{"--o " + outputPrefix} \
+ ~{"--datasets " + datasetFile}
+ }
+
+ output {
+ File outputAnnotation = outputPrefix + "_talon_read_annot.tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ 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"
+ }
+ outputAnnotation: {
+ description: "Read-specific annotation information from a TALON database.",
+ category: "required"
+ }
}
}
task InitializeTalonDatabase {
input {
File GTFfile
- String outputPrefix
String genomeBuild
String annotationVersion
Int minimumLength = 300
String novelIDprefix = "TALON"
Int cutoff5p = 500
Int cutoff3p = 300
+ String outputPrefix
Int cores = 1
String memory = "10G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
set -e
mkdir -p $(dirname ~{outputPrefix})
- initialize_talon_database \
+ talon_initialize_database \
~{"--f=" + GTFfile} \
- ~{"--o=" + outputPrefix} \
~{"--g=" + genomeBuild} \
~{"--a=" + annotationVersion} \
~{"--l=" + minimumLength} \
~{"--idprefix=" + novelIDprefix} \
~{"--5p=" + cutoff5p} \
- ~{"--3p=" + cutoff3p}
+ ~{"--3p=" + cutoff3p} \
+ ~{"--o=" + outputPrefix}
}
output {
@@ -213,41 +315,62 @@ task InitializeTalonDatabase {
}
parameter_meta {
- GTFfile: "GTF annotation containing genes, transcripts, and edges."
- outputPrefix: "Output directory path + output file prefix."
- genomeBuild: "Name of genome build that the GTF file is based on (ie hg38)."
- annotationVersion: "Name of supplied annotation (will be used to label data)."
- minimumLength: "Minimum required transcript length."
- novelIDprefix: "Prefix for naming novel discoveries in eventual TALON runs."
- cutoff5p: "Maximum allowable distance (bp) at the 5' end during annotation."
- cutoff3p: "Maximum allowable distance (bp) at the 3' end during annotation."
-
- outputDatabase: "TALON database."
+ 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"
+ }
+ 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"
+ }
+ outputDatabase: {
+ description: "TALON database.",
+ category: "required"
+ }
}
}
-task MapAntisenseGenesToSense {
+task ReformatGtf {
input {
- File databaseFile
- String outputPrefix
- String annotationVersion
+ File GTFfile
Int cores = 1
String memory = "4G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
set -e
- mkdir -p $(dirname ~{outputPrefix})
- map_antisense_genes_to_sense \
- ~{"--db=" + databaseFile} \
- ~{"--o=" + outputPrefix} \
- ~{"-a " + annotationVersion}
+ talon_reformat_gtf \
+ ~{"-gtf " + GTFfile}
}
output {
- File outputAntisenseMapFile = outputPrefix + "_antisense_mapping.gtf"
+ File outputReformattedGTF = GTFfile
}
runtime {
@@ -257,31 +380,32 @@ task MapAntisenseGenesToSense {
}
parameter_meta {
- databaseFile: "TALON database."
- outputPrefix: "Output directory path + output file prefix."
- annotationVersion: "Which annotation version to use."
-
- outputAntisenseMapFile: "IDs of the sense gene for every antisense gene in the database."
+ GTFfile: {
+ description: "GTF annotation containing genes, transcripts, and edges.",
+ category: "required"
+ }
}
}
task SummarizeDatasets {
input {
File databaseFile
+ Boolean setVerbose = false
String outputPrefix
File? datasetGroupsCSV
Int cores = 1
String memory = "4G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
set -e
mkdir -p $(dirname ~{outputPrefix})
- summarize_datasets \
+ talon_summarize \
~{"--db " + databaseFile} \
+ ~{true="--verbose" false="" setVerbose} \
~{"--o " + outputPrefix} \
~{"--groups " + datasetGroupsCSV}
}
@@ -297,11 +421,26 @@ task SummarizeDatasets {
}
parameter_meta {
- databaseFile: "TALON database."
- outputPrefix: "Output directory path + output file prefix."
- datasetGroupsCSV: "File of comma-delimited dataset groups to process together."
-
- outputSummaryFile: "Tab-delimited file of gene and transcript counts for each dataset."
+ 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"
+ }
+ outputSummaryFile: {
+ description: "Tab-delimited file of gene and transcript counts for each dataset.",
+ category: "required"
+ }
}
}
@@ -310,16 +449,16 @@ task Talon {
File SAMfile
File configFile
File databaseFile
- String outputPrefix
String genomeBuild
- String configFileName = basename(configFile)
- String SAMfileName = basename(SAMfile)
Float minimumCoverage = 0.9
Int minimumIdentity = 0
+ String outputPrefix
+ String configFileName = basename(configFile)
+ String SAMfileName = basename(SAMfile)
Int cores = 1
String memory = "20G"
- String dockerImage = "biocontainers/talon:v4.2_cv2"
+ String dockerImage = "biocontainers/talon:v4.4_cv1"
}
command {
@@ -330,10 +469,11 @@ task Talon {
talon \
~{"--f " + configFileName} \
~{"--db " + databaseFile} \
- ~{"--o " + outputPrefix} \
~{"--build " + genomeBuild} \
+ ~{"--threads " + cores} \
~{"--cov " + minimumCoverage} \
- ~{"--identity " + minimumIdentity}
+ ~{"--identity " + minimumIdentity} \
+ ~{"--o " + outputPrefix}
}
output {
@@ -348,15 +488,41 @@ task Talon {
}
parameter_meta {
- SAMfile: "Input SAM file, same one as described in configFile."
- configFile: "Dataset config file."
- databaseFile: "TALON database. Created using initialize_talon_database.py."
- outputPrefix: "Output directory path + output file prefix."
- genomeBuild: "Genome build (i.e. hg38) to use."
- minimumCoverage: "Minimum alignment coverage in order to use a SAM entry."
- minimumIdentity: "Minimum alignment identity in order to use a SAM entry."
-
- outputUpdatedDatabase: "Updated TALON database."
- outputLog: "Log file from TALON run."
+ SAMfile: {
+ description: "Input SAM file, same one as described in configFile.",
+ category: "required"
+ }
+ configFile: {
+ description: "Dataset config file (comma-delimited).",
+ 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"
+ }
+ outputPrefix: {
+ description: "Output directory path + output file prefix.",
+ category: "required"
+ }
+ outputUpdatedDatabase: {
+ description: "Updated TALON database.",
+ category: "required"
+ }
+ outputLog: {
+ description: "Log file from TALON run.",
+ category: "required"
+ }
}
}