diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7813c2090dea4db071f71744add6e89cdfd1516c..9a546718279bc853ad32fff24257e442cda43271 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,11 @@ that users understand how the changes affect the new version.
version 4.0.0-develop
---------------------------
++ TALON: Update `FilterTalonTranscripts` to new version, which removes the
+ pairingsFile and replaces this with datasetsFile.
++ TALON: Add `GetSpliceJunctions` & `LabelReads` tasks.
++ TALON: Update to version 5.0.
++ Add tasks for pbmm2, the PacBio wrapper for minimap2.
+ Update the image for chunked-scatter and make use of new features from 0.2.0.
+ Tuned resource requirements for GATK VariantEval, MultiQC, Picard metrics and
STAR.
diff --git a/pbmm2.wdl b/pbmm2.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..84fbd2d08e32c9b9676e5b24f6d6c0843bb95dce
--- /dev/null
+++ b/pbmm2.wdl
@@ -0,0 +1,74 @@
+version 1.0
+
+# Copyright (c) 2020 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 Mapping {
+ input {
+ String presetOption
+ Boolean sort=true
+ String sample
+ File referenceMMI
+ File queryFile
+
+ Int cores = 4
+ String memory = "30G"
+ Int timeMinutes = 1 + ceil(size(queryFile, "G") * 200 / cores)
+ String dockerImage = "quay.io/biocontainers/pbmm2:1.3.0--h56fc30b_1"
+ }
+
+ command {
+ pbmm2 align \
+ --preset ~{presetOption} \
+ ~{true="--sort" false="" sort} \
+ -j ~{cores} \
+ ~{referenceMMI} \
+ ~{queryFile} \
+ ~{sample}.align.bam
+ }
+
+ output {
+ File outputAlignmentFile = sample + ".align.bam"
+ File outputIndexFile = sample + ".align.bam.bai"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ presetOption: {description: "This option applies multiple options at the same time.", category: "required"}
+ sort: {description: "Sort the output bam file.", category: "advanced"}
+ sample: {description: "Name of the sample"}
+ referenceMMI: {description: "MMI file for the reference.", category: "required"}
+ queryFile: {description: "BAM file with reads to align against the reference.", category: "required"}
+ cores: {description: "The number of cores to be used.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # output
+ outputAlignmentFile: {description: "Mapped bam file."}
+ outputIndexFile: {description: "Bam index file."}
+ }
+}
diff --git a/scripts b/scripts
index b83da72b9b43b956a3062b78fb08044eb9fae464..325a129c14de56b2055ee0e9e0da7dc74df5fec4 160000
--- a/scripts
+++ b/scripts
@@ -1 +1 @@
-Subproject commit b83da72b9b43b956a3062b78fb08044eb9fae464
+Subproject commit 325a129c14de56b2055ee0e9e0da7dc74df5fec4
diff --git a/talon.wdl b/talon.wdl
index 98e0c13a7af5ebe3029f02522dbcdcbbd35c905c..a469ddbac873944a9236cd53611b8fd8b46c7981 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -32,7 +32,7 @@ task CreateAbundanceFileFromDatabase {
String memory = "4G"
Int timeMinutes = 30
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -88,7 +88,7 @@ task CreateGtfFromDatabase {
String memory = "4G"
Int timeMinutes = 30
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -137,12 +137,16 @@ task FilterTalonTranscripts {
File databaseFile
String annotationVersion
String outputPrefix
+ Float maxFracA = 0.5
+ Int minCount = 5
+ Boolean allowGenomic = false
- File? pairingsFile
+ File? datasetsFile
+ Int? minDatasets
String memory = "4G"
Int timeMinutes = 30
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -152,7 +156,11 @@ task FilterTalonTranscripts {
--db=~{databaseFile} \
-a ~{annotationVersion} \
~{"--o=" + outputPrefix + "_whitelist.csv"} \
- ~{"-p " + pairingsFile}
+ --maxFracA=~{maxFracA} \
+ --minCount=~{minCount} \
+ ~{true="--allowGenomic" false="" allowGenomic} \
+ --datasets=~{datasetsFile} \
+ --minDatasets=~{minDatasets}
}
output {
@@ -170,7 +178,11 @@ task FilterTalonTranscripts {
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"}
+ maxFracA: {description: "Maximum fraction of As to allow in the window located immediately after any read assigned to a novel transcript.", category: "advanced"}
+ minCount: {description: "Number of minimum occurrences required for a novel transcript PER dataset.", category: "advanced"}
+ allowGenomic: {description: "If this option is set, transcripts from the Genomic novelty category will be permitted in the output.", category: "advanced"}
+ datasetsFile: {description: "Datasets to include.", category: "advanced"}
+ minDatasets: {description: "Minimum number of datasets novel transcripts must be found in.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
@@ -190,7 +202,7 @@ task GetReadAnnotations {
String memory = "4G"
Int timeMinutes = 30
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -228,6 +240,57 @@ task GetReadAnnotations {
}
}
+task GetSpliceJunctions {
+ input {
+ File SJinformationFile
+ String inputFileType = "db"
+ File referenceGTF
+ String runMode = "intron"
+ String outputPrefix
+
+ String memory = "4G"
+ Int timeMinutes = 30
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
+ }
+
+ Map[String, String] SJfileType = {"db": "--db", "gtf": "--gtf"}
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ talon_get_sjs \
+ ~{SJfileType[inputFileType] + SJinformationFile} \
+ --ref ~{referenceGTF} \
+ --mode ~{runMode} \
+ --outprefix ~{outputPrefix}
+ }
+
+ output {
+ File outputSJfile = outputPrefix + "_" + runMode + "s.tsv"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ SJinformationFile: {description: "TALON GTF file or database from which to extract exons/introns.", category: "required"}
+ inputFileType: {description: "The file type of SJinformationFile.", category: "common"}
+ referenceGTF: {description: "GTF reference file (ie GENCODE).", category: "required"}
+ runMode: {description: "Determines whether to include introns or exons in the output.", category: "common"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputSJfile: {description: "File containing locations, novelty and transcript assignments of exons/introns."}
+ }
+}
+
task InitializeTalonDatabase {
input {
File GTFfile
@@ -241,7 +304,7 @@ task InitializeTalonDatabase {
String memory = "10G"
Int timeMinutes = 60
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -287,13 +350,72 @@ task InitializeTalonDatabase {
}
}
+task LabelReads {
+ input {
+ File SAMfile
+ File referenceGenome
+ Int fracaRangeSize = 20
+ String tmpDir = "./tmp_label_reads"
+ Boolean deleteTmp = true
+ String outputPrefix
+
+ Int threads = 4
+ String memory = "25G"
+ Int timeMinutes = 2880
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ talon_label_reads \
+ --f=~{SAMfile} \
+ --g=~{referenceGenome} \
+ --t=~{threads} \
+ --ar=~{fracaRangeSize} \
+ --tmpDir=~{tmpDir} \
+ ~{true="--deleteTmp" false="" deleteTmp} \
+ --o=~{outputPrefix}
+ }
+
+ output {
+ File outputLabeledSAM = outputPrefix + "_labeled.sam"
+ File outputReadLabels = outputPrefix + "_read_labels.tsv"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ SAMfile: {description: "SAM file of transcripts.", category: "required"}
+ referenceGenome: {description: "Reference genome fasta file.", category: "required"}
+ fracaRangeSize: {description: "Size of post-transcript interval to compute fraction.", category: "common"}
+ tmpDir: {description: "Path to directory for tmp files.", category: "advanced"}
+ deleteTmp: {description: "If set, tmp dir will be removed.", category: "advanced"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ threads: {description: "The number of threads to be used.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputLabeledSAM: {description: "SAM file with labeled transcripts."}
+ outputReadLabels: {description: "Tabular file with fraction description per read."}
+ }
+}
+
task ReformatGtf {
input {
File GTFfile
String memory = "4G"
Int timeMinutes = 30
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -334,7 +456,7 @@ task SummarizeDatasets {
String memory = "4G"
Int timeMinutes = 50
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command {
@@ -383,10 +505,10 @@ task Talon {
Float minimumIdentity = 0.8
String outputPrefix
- Int cores = 4
+ Int threads = 4
String memory = "25G"
Int timeMinutes = 2880
- String dockerImage = "biocontainers/talon:v4.4.2_cv1"
+ String dockerImage = "biocontainers/talon:v5.0_cv1"
}
command <<<
@@ -405,7 +527,7 @@ task Talon {
~{"--f " + outputPrefix + "/talonConfigFile.csv"} \
--db ~{databaseFile} \
--build ~{genomeBuild} \
- --threads ~{cores} \
+ --threads ~{threads} \
--cov ~{minimumCoverage} \
--identity ~{minimumIdentity} \
~{"--o " + outputPrefix + "/run"}
@@ -419,7 +541,7 @@ task Talon {
}
runtime {
- cpu: cores
+ cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
@@ -435,7 +557,7 @@ task Talon {
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"}
- cores: {description: "The number of cores to be used.", category: "advanced"}
+ threads: {description: "The number of threads to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}