Add WDL task for TALON

talon.wdl

+version 1.0
+
+# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task CreateAbundanceFileFromDatabase {
+    input {
+        File databaseFile
+        String outputPrefix
+        String genomeBuild
+        String annotationVersion
+        Boolean filterTranscripts = false
+
+        File? filterPairingsFile
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        create_abundance_file_from_database \
+        ~{"--db=" + databaseFile} \
+        ~{"--o=" + outputPrefix} \
+        ~{"-b " + genomeBuild} \
+        ~{"-a " + annotationVersion} \
+        ~{true="--filter" false="" filterTranscripts} \
+        ~{"-p " + filterPairingsFile}
+    }
+
+    output {
+        File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+    }
+}
+
+task CreateGtfAbundanceFromDatabase {
+    input {
+        File databaseFile
+        String outputPrefix
+        String genomeBuild
+        String annotationVersion
+        Boolean filterTranscripts = false
+
+        File? filterPairingsFile
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        create_GTF_abundance_from_database \
+        ~{"--db=" + databaseFile} \
+        ~{"--o=" + outputPrefix} \
+        ~{"-b " + genomeBuild} \
+        ~{"-a " + annotationVersion} \
+        ~{true="--filter" false="" filterTranscripts} \
+        ~{"-p " + filterPairingsFile}
+    }
+
+    output {
+        File outputGTFfile = outputPrefix + "_talon_observedOnly.gtf"
+        File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+    }
+}
+
+task CreateGtfFromDatabase {
+    input {
+        File databaseFile
+        String outputPrefix
+        String genomeBuild
+        String annotationVersion
+        Boolean observedInDataset = false
+
+        File? whitelistFile
+        File? datasetFile
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        create_GTF_from_database \
+        ~{"--db=" + databaseFile} \
+        ~{"--o=" outputPrefix} \
+        ~{"-b " + genomeBuild} \
+        ~{"-a " + annotationVersion} \
+        ~{"--whitelist=" + whitelistFile} \
+        ~{true="--observed" false="" observedInDataset} \
+        ~{"-d " + datasetFile}
+    }
+
+    output {
+        File outputGTFfile = outputPrefix + "_talon.gtf"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+
+        outputGTFfile: "The genes, transcripts, and exons stored a TALON database in GTF format."
+    }
+}
+
+task InitializeTalonDatabase {
+    input {
+        File GTFfile
+        String outputPrefix
+        String genomeBuild
+        String annotationVersion
+        Int minimumLength = 300
+        String novelIDprefix = "TALON"
+        Int cutoff5p = 500
+        Int cutoff3p = 300
+
+        Int cores = 1
+        Int memory = 10
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        initialize_talon_database \
+        ~{"--f=" + GTFfile} \
+        ~{"--o=" + outputPrefix} \
+        ~{"--g=" + genomeBuild} \
+        ~{"--a=" + annotationVersion} \
+        ~{"--l=" +  minimumLength} \
+        ~{"--idprefix=" + novelIDprefix} \
+        ~{"--5p=" + cutoff5p} \
+        ~{"--3p=" + cutoff3p}
+    }
+
+    output {
+        File outputDatabase = outputPrefix + ".db"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+    }
+}
+
+task MapAntisenseGenesToSense {
+    input {
+        File databaseFile
+        String outputPrefix
+        String annotationVersion
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        map_antisense_genes_to_sense \
+        ~{"--db=" + databaseFile} \
+        ~{"--o=" + outputPrefix} \
+        ~{"-a " + annotationVersion}
+    }
+
+    output {
+        File outputAntisenseMapFile = outputPrefix + "_antisense_mapping.gtf"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+    }
+}
+
+task SummarizeDatasets {
+    input {
+        File databaseFile
+        String outputPrefix
+
+        File? datasetGroupsCSV
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        summarize_datasets \
+        ~{"--db " + databaseFile} \
+        ~{"--o " + outputPrefix} \
+        ~{"--groups " + datasetGroupsCSV}
+    }
+
+    output {
+        File outputSummaryFile = outputPrefix + "_talon_summary.tsv"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+    }
+}
+
+task Talon {
+    input {
+        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
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "biocontainers/talon:v4.2_cv2"
+    }
+
+    command {
+        set -e pipefail
+        mkdir -p $(dirname ~{outputPrefix})
+        mv ${configFile} ./${configFileName}
+        mv ${SAMfile} ./${SAMfileName}
+        talon \
+        ~{"--f " + configFileName} \
+        ~{"--db " + databaseFile} \
+        ~{"--o " outputPrefix} \
+        ~{"--build " + genomeBuild} \
+        ~{"--cov " + minimumCoverage} \
+        ~{"--identity " + minimumIdentity}
+    }
+
+    output {
+        File outputUpdatedDatabase = databaseFile
+        File outputLog = outputPrefix + "_talon_QC.log"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    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."
+    }
+}