diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1becd5aeeef53fc73e475326c2264366f779128f..28f2e77056d79e76f6ca8fd1363df23725c05afb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
version 2.2.0-dev
---------------------------
++ Update centrifuge tasks.
+ Removed unused "cores" inputs from transcriptclean tasks.
+ Removed unused "cores" inputs from talon tasks.
+ Removed unused "threads" input from ModifyStrelka.
diff --git a/centrifuge.wdl b/centrifuge.wdl
index ec6652f93de5f29c1338f7d7ee7d7f3e9192d0f0..5110b8723e20a2a964032c88921bbb917d0fc949 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -1,124 +1,199 @@
version 1.0
-# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
+# Copyright (c) 2018 Sequencing Analysis Support Core - Leiden University Medical Center
#
-# Tasks from centrifuge
+# 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 Build {
input {
+ Boolean disableDifferenceCover = false
File conversionTable
File taxonomyTree
- File inputFasta
- String centrifugeIndexBase
- String? preCommand
- String centrifugeBuildExecutable = "centrifuge-build"
- #Boolean? c = false
- Boolean largeIndex = false
- Boolean noAuto = false
- Int? bMax
- Int? bMaxDivn
- Boolean noDiffCover = false
- Boolean noRef = false
- Boolean justRef = false
- Int? offRate
- Int? fTabChars
- File? nameTable
- File? sizeTable
- Int? seed
+ File nameTable
+ File referenceFile
+ String indexBasename = "centrifuge_index"
+ String outputPrefix
+
+ Int? offrate
+ Int? ftabChars
Int? kmerCount
+ File? sizeTable
- Int threads = 8
+ Int threads = 5
String memory = "20G"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
}
command {
- set -e -o pipefail
- ~{preCommand}
- ~{"mkdir -p $(dirname " + centrifugeIndexBase + ")"}
- ~{centrifugeBuildExecutable} \
- ~{true='--large-index' false='' largeIndex} \
- ~{true='--noauto' false='' noAuto} \
- ~{'--bmax ' + bMax} \
- ~{'--bmaxdivn ' + bMaxDivn} \
- ~{true='--nodc' false='' noDiffCover} \
- ~{true='--noref' false='' noRef} \
- ~{true='--justref' false='' justRef} \
- ~{'--offrate ' + offRate} \
- ~{'--ftabchars ' + fTabChars} \
- ~{'--name-table ' + nameTable } \
- ~{'--size-table ' + sizeTable} \
- ~{'--seed ' + seed} \
- ~{'--kmer-count' + kmerCount} \
- ~{'--threads ' + threads} \
- --conversion-table ~{conversionTable} \
- --taxonomy-tree ~{taxonomyTree} \
- ~{inputFasta} \
- ~{centrifugeIndexBase}
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ centrifuge-build \
+ ~{"--threads " + threads} \
+ ~{true="--nodc" false="" disableDifferenceCover} \
+ ~{"--offrate " + offrate} \
+ ~{"--ftabchars " + ftabChars} \
+ ~{"--kmer-count " + kmerCount} \
+ ~{"--size-table " + sizeTable} \
+ ~{"--conversion-table " + conversionTable} \
+ ~{"--taxonomy-tree " + taxonomyTree} \
+ ~{"--name-table " + nameTable} \
+ ~{referenceFile} \
+ ~{outputPrefix + "/" + indexBasename}
+ }
+
+ output {
+ Array[File] outputIndex = glob(outputPrefix + "/" + indexBasename + "*.cf")
}
runtime {
cpu: threads
memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ disableDifferenceCover: {description: "Disable use of the difference-cover sample.", category: "required"}
+ conversionTable: {description: "List of UIDs (unique ID) and corresponding taxonomic IDs.", category: "required"}
+ taxonomyTree: {description: "Taxonomic tree (e.g. nodes.dmp).", category: "required"}
+ nameTable: {description: "Name table (e.g. names.dmp).", category: "required"}
+ referenceFile: {description: "A comma-separated list of FASTA files containing the reference sequences to be aligned to.", category: "required"}
+ indexBasename: {description: "The basename of the index files to write.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ offrate: {description: "The number of rows marked by the indexer.", category: "common"}
+ ftabChars: {description: "Calculate an initial BW range with respect to this character.", category: "common"}
+ kmerCount: {description: "Use <int> as kmer-size for counting the distinct number of k-mers in the input sequences.", category: "common"}
+ sizeTable: {description: "List of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", category: "common"}
}
}
task Classify {
input {
- String outputDir
- Boolean compressOutput = true
- String? preCommand
+ String inputFormat = "fastq"
+ Boolean phred64 = false
+ Int minHitLength = 22
String indexPrefix
- Array[File]? unpairedReads
Array[File]+ read1
- Array[File]? read2
- Boolean? fastaInput
- # Variables for handling output
+ String outputPrefix
+ String outputName = basename(outputPrefix)
- String? metFilePath # If this is specified, the report file is empty
- Int? assignments
- Int? minHitLen
- Int? minTotalLen
- Array[String]? hostTaxIds
- Array[String]? excludeTaxIds
+ Array[File]? read2
+ Int? trim5
+ Int? trim3
+ Int? reportMaxDistinct
+ String? hostTaxIDs
+ String? excludeTaxIDs
Int threads = 4
- String memory = "8G"
+ String memory = "16G"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
}
- String outputFilePath = outputDir + "/centrifuge.out"
- String reportFilePath = outputDir + "/centrifuge_report.tsv"
- String finalOutputPath = if (compressOutput == true)
- then outputFilePath + ".gz"
- else outputFilePath
+ Map[String, String] inputFormatOptions = {"fastq": "-q", "fasta": "-f", "qseq": "--qseq", "raw": "-r", "sequences": "-c"}
command {
- set -e -o pipefail
- mkdir -p ~{outputDir}
- ~{preCommand}
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
centrifuge \
- ~{"-p " + threads} \
+ ~{inputFormatOptions[inputFormat]} \
+ ~{true="--phred64" false="--phred33" phred64} \
+ ~{"--min-hitlen " + minHitLength} \
+ ~{"--met-file " + outputPrefix + "/" + outputName + "_alignment_metrics.tsv"} \
+ ~{"--threads " + threads} \
+ ~{"--trim5 " + trim5} \
+ ~{"--trim3 " + trim3} \
+ ~{"-k " + reportMaxDistinct} \
+ ~{"--host-taxids " + hostTaxIDs} \
+ ~{"--exclude-taxids " + excludeTaxIDs} \
~{"-x " + indexPrefix} \
- ~{true="-f" false="" fastaInput} \
- ~{true="-k" false="" defined(assignments)} ~{assignments} \
- ~{true="-1" false="-U" defined(read2)} ~{sep=',' read1} \
- ~{true="-2" false="" defined(read2)} ~{sep=',' read2} \
- ~{true="-U" false="" length(select_first([unpairedReads])) > 0} ~{sep=',' unpairedReads} \
- ~{"--report-file " + reportFilePath} \
- ~{"--min-hitlen " + minHitLen} \
- ~{"--min-totallen " + minTotalLen} \
- ~{"--met-file " + metFilePath} \
- ~{true="--host-taxids " false="" defined(hostTaxIds)} ~{sep=',' hostTaxIds} \
- ~{true="--exclude-taxids " false="" defined(excludeTaxIds)} ~{sep=',' excludeTaxIds} \
- ~{true="| gzip -c >" false="-S" compressOutput} ~{finalOutputPath}
+ ~{true="-1 " false="-U " defined(read2)} ~{sep="," read1} \
+ ~{"-2 "} ~{sep="," read2} \
+ ~{"-S " + outputPrefix + "/" + outputName + "_classification.tsv"} \
+ ~{"--report-file " + outputPrefix + "/" + outputName + "_output_report.tsv"}
}
output {
- File classifiedReads = finalOutputPath
- File reportFile = reportFilePath
+ File outputMetrics = outputPrefix + "/" + outputName + "_alignment_metrics.tsv"
+ File outputClassification = outputPrefix + "/" + outputName + "_classification.tsv"
+ File outputReport = outputPrefix + "/" + outputName + "_output_report.tsv"
}
runtime {
cpu: threads
memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputFormat: {description: "The format of the read file(s).", category: "required"}
+ phred64: {description: "If set to true, Phred+64 encoding is used.", category: "required"}
+ minHitLength: {description: "Minimum length of partial hits.", category: "required"}
+ indexPrefix: {description: "The basename of the index for the reference genomes.", category: "required"}
+ read1: {description: "List of files containing mate 1s, or unpaired reads.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ outputName: {description: "The base name of the outputPrefix.", category: "required"}
+ read2: {description: "List of files containing mate 2s.", category: "common"}
+ trim5: {description: "Trim <int> bases from 5' (left) end of each read before alignment.", category: "common"}
+ trim3: {description: "Trim <int> bases from 3' (right) end of each read before alignment.", category: "common"}
+ reportMaxDistinct: {description: "It searches for at most <int> distinct, primary assignments for each read or pair.", category: "common"}
+ hostTaxIDs: {description: "A comma-separated list of taxonomic IDs that will be preferred in classification procedure.", category: "common"}
+ excludeTaxIDs: {description: "A comma-separated list of taxonomic IDs that will be excluded in classification procedure.", category: "common"}
+ }
+}
+
+task Inspect {
+ input {
+ String printOption = "fasta"
+ String indexBasename
+ String outputPrefix
+
+ Int? across
+
+ String memory = "4G"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
+ }
+
+ Map[String, String] outputOptions = {"fasta": "", "names": "--names", "summary": "--summary", "conversionTable": "--conversion-table", "taxonomyTree": "--taxonomy-tree", "nameTable": "--name-table", "sizeTable": "--size-table"}
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ centrifuge-inspect \
+ ~{outputOptions[printOption]} \
+ ~{"--across " + across} \
+ ~{indexBasename} \
+ > ~{outputPrefix + "/" + printOption}
+ }
+
+ output {
+ File outputInspect = outputPrefix + "/" + printOption
+ }
+
+ runtime {
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ printOption: {description: "The output option for inspect (fasta, summary, conversionTable, taxonomyTree, nameTable, sizeTable)", category: "required"}
+ indexBasename: {description: "The basename of the index to be inspected.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ across: {description: "When printing FASTA output, output a newline character every <int> bases.", category: "common"}
}
}