Merge remote-tracking branch 'origin/develop' into refOptional

CHANGELOG.md

@@ -12,6 +12,13 @@ version 5.0.0-dev
 ---------------------------
 + GffCompare: Make the `referenceAnnotation` input optional.
 + Stringtie: Add the `minimumCoverage` input.
++ UMI-tools: update default dockerImage to use umitools v1.1.1 with correct samtools version (1.10)
++ UMI-tools: re-introduce samtools indexing
++ UMI-tools: update default dockerImage to use umitools v1.1.1
++ UMI-tools dedup: Add tempdir
++ Update BCFTOOLS view: add options for filtering (include, exclude, excludeUncalled).
++ Duphold: add duphold.wdl.
++ Add new wdl file prepareShiny.wdl for creating input files for shiny app.
 + mergePacBio: Rename `mergedReport` to `outputPathMergedReport`.
 + Lima: Fix copy commands.
 + Fixed the `size` call in the default for gffread's timeMinutes, to retrieve

bcftools.wdl

@@ -290,6 +290,10 @@ task View {
     input {
         File inputFile
         String outputPath = "output.vcf"
+        Boolean excludeUncalled = false
+
+        String? exclude
+        String? include
 
         String memory = "256M"
         Int timeMinutes = 1 + ceil(size(inputFile, "G"))
@@ -302,6 +306,9 @@ task View {
         set -e
         mkdir -p "$(dirname ~{outputPath})"
         bcftools view \
+        ~{"--exclude " + exclude} \
+        ~{"--include " + include} \
+        ~{true="--exclude-uncalled" false="" excludeUncalled} \
         -o ~{outputPath} \
         -O ~{true="z" false="v" compressed} \
         ~{inputFile}
@@ -324,6 +331,9 @@ task View {
         # inputs
         inputFile: {description: "A vcf or bcf file.", category: "required"}
         outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+        include: {description: "Select sites for which the expression is true (see man page for details).", category: "advanced"}
+        exclude: {description: "Exclude sites for which the expression is true (see man page for details).", category: "advanced"}
+        excludeUncalled: {description: "Exclude sites without a called genotype (see man page for details).", category: "advanced"}
         memory: {description: "The amount of memory this job will use.", 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"}

duphold.wdl

+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 Duphold {
+    input {
+        File inputVcf
+        File bamFile
+        File bamIndex
+        File referenceFasta
+        File referenceFastaFai
+        String sample
+        String outputPath = "./duphold.vcf"
+
+        String memory = "15G"
+        Int timeMinutes = 1440
+        String dockerImage = "quay.io/biocontainers/duphold:0.2.1--h516909a_1"
+    }
+
+    command {
+        set -e
+        mkdir -p "$(dirname ~{outputPath})"
+        export DUPHOLD_SAMPLE_NAME=~{sample}
+        duphold \
+        -v ~{inputVcf} \
+        -b ~{bamFile} \
+        -f ~{referenceFasta} \
+        -o ~{outputPath}
+    }
+
+    output {
+        File outputVcf = outputPath
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        # inputs
+        inputVcf: {description: "The VCF file to process.", category: "required"}
+        bamFile: {description: "The bam file to process.", category: "required"}
+        bamIndex: {description: "The index of the bam file.", category: "required"}
+        referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
+        referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
+        sample: {description: "The name of the sample.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+        memory: {description: "The memory required to run the programs.", category: "advanced"}
+        timeMinutes: {description: "The maximum duration (in minutes) the tool is allowed to run.", 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
+        outputVcf: {description: "Duphold annotated VCF file."}
+    }
+}

prepareShiny.wdl

+version 1.0
+
+# Copyright (c) 2017 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 CreateDesignMatrix {
+    input {
+        File countTable
+        String shinyDir = "."
+
+        String memory = "5G"
+        Int timeMinutes = 30
+        String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
+    }
+
+    command {
+        set -e
+        mkdir -p ~{shinyDir}
+        predex design \
+        --input ~{countTable} \
+        --output ~{shinyDir}
+    }
+
+    output {
+        File dgeDesign = shinyDir + "/design_matrix.tsv"
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        # inputs
+        countTable: {description: "The created count table from HTseq.", category: "required"}
+        shinyDir: {description: "The directory to write the output to.", category: "required"}
+        memory: {description: "The amount of memory this job will use.", 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
+        dgeDesign: {description: "Design matrix template to add sample information for DGE analysis."}
+    }
+}
+
+task CreateAnnotation {
+    input {
+        File referenceFasta
+        File referenceGtfFile
+        String shinyDir = "."
+
+        String memory = "5G"
+        Int timeMinutes = 30
+        String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
+    }
+
+    command {
+        set -e
+        mkdir -p ~{shinyDir}
+        predex annotation \
+        --fasta ~{referenceFasta} \
+        --gtf ~{referenceGtfFile} \
+        --output ~{shinyDir}
+    }
+
+    output {        
+        File dgeAnnotation = shinyDir + "/annotation.tsv"
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        # inputs
+        referenceFasta: {description: "The reference Fasta file.", category: "required"}
+        referenceGtfFile: {description: "The reference GTF file.", category: "required"}
+        shinyDir: {description: "The directory to write the output to.", category: "required"}
+        memory: {description: "The amount of memory this job will use.", 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
+        dgeAnnotation: {description: "Annotation file for DGE analysis."}
+    }
+}

umi-tools.wdl

@@ -31,7 +31,7 @@ task Extract {
         Boolean threePrime = false
 
         Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
-        String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
+        String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
     }
 
     command {
@@ -78,6 +78,8 @@ task Dedup {
         File inputBam
         File inputBamIndex
         String outputBamPath
+        String tmpDir = "./umiToolsDedupTmpDir"
+
         Boolean paired = true
 
         String? umiSeparator
@@ -85,21 +87,21 @@ task Dedup {
 
         String memory = "25G"
         Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30)
-        # Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9).
-        String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
+        String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
     }
 
     String outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
 
     command {
         set -e
-        mkdir -p "$(dirname ~{outputBamPath})"
+        mkdir -p "$(dirname ~{outputBamPath})" "~{tmpDir}"
         umi_tools dedup \
-        --stdin ~{inputBam} \
-        --stdout ~{outputBamPath} \
+        --stdin=~{inputBam} \
+        --stdout=~{outputBamPath} \
         ~{"--output-stats " + statsPrefix} \
         ~{"--umi-separator=" + umiSeparator} \
-        ~{true="--paired" false="" paired}
+        ~{true="--paired" false="" paired} \
+        --temp-dir=~{tmpDir}
         samtools index ~{outputBamPath} ~{outputBamIndex}
     }
 
@@ -122,6 +124,7 @@ task Dedup {
         inputBam: {description: "The input BAM file.", categrory: "required"}
         inputBamIndex: {description: "The index for the ipnut BAM file.", cateogry: "required"}
         outputBamPath: {description: "The location to write the output BAM file to.", category: "required"}
+        tmpDir: {description: "Temporary directory.", category: "advanced"}
         paired: {description: "Whether or not the data is paired.", category: "common"}
         umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
         statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}