biowdl · hexylena · Jul 29, 2025 · Apr 23, 2025 · Apr 23, 2025 · Apr 23, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -50,6 +50,8 @@ version 6.0.0-dev
 + Fixed bug whereby `samtools.Fastq` could produce out of sync R1/R2 when used with an unsorted bam input. `samtools collate` is now used by default to group reads by readname in order to avoid this issue.
 + New samtools task: split.
 + Update `bedtools.Intersect` to support `-wa`, `-wb`, and `-s` flags.
++ Add `biopet.ValidateFastq` to check your fastq files for pairing and other correctness.
++ **Breaking**: `samtools.Fastq` now requires defining your singleton read location. This only affects you if you were previously using this task with only a single output read file.
 + Deprecate `modkit.Pileup`'s bedGraph option, it is now output by default.
 + Add support for filterThreshold/filterPercent for `modkit.Pileup`.
 + Add `modkit.Summary` task.

diff --git a/biopet.wdl b/biopet.wdl
@@ -0,0 +1,60 @@
+version 1.0
+
+# Copyright (c) 2025 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 ValidateFastq {
+    input {
+        File inputRead1
+        File? inputRead2
+
+        String memory = "1GiB"
+        Int timeMinutes = 5 + ceil(size(inputRead1, "GiB"))
+        String dockerImage = "quay.io/biocontainers/biopet-validatefastq:0.1.1--hdfd78af_3"
+    }
+
+    command {
+        set -e
+        java -jar /usr/local/share/biopet-validatefastq-0.1.1-3/validatefastq-assembly-0.1.1.jar \
+        --fastq1 ~{inputRead1} \
+        ~{"--fastq2 " + inputRead2}
+    }
+
+    output {
+    }
+
+    runtime {
+        cpu: 1
+        memory: memory
+        docker: dockerImage
+        time_minutes: timeMinutes
+    }
+
+    parameter_meta {
+        # inputs
+        inputRead1: {description: "The location of the first FASTQ file (first reads for pairs, in case of paired-end sequencing).", category: "required"}
+        inputRead2: {description: "The location of the paired end reads.", category: "common"}
+
+        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"}
+    }
+}
diff --git a/samtools.wdl b/samtools.wdl
@@ -167,6 +167,7 @@ task Fastq {
         String outputRead1
         String? outputRead2
         String? outputRead0
+        String? outputReadS
         Boolean appendReadNumber = false
         Boolean outputQuality = false
 
@@ -186,9 +187,10 @@ task Fastq {
         mkdir -p "$(dirname ~{outputRead1})"
         samtools collate -u -O ~{inputBam} | \
         samtools fastq \
-        ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
+        ~{"-1 " + outputRead1} \
         ~{"-2 " + outputRead2} \
         ~{"-0 " + outputRead0} \
+        ~{"-s " + outputReadS} \
         ~{"-f " + includeFilter} \
         ~{"-F " + excludeFilter} \
         ~{"-G " + excludeSpecificFilter} \
@@ -202,6 +204,7 @@ task Fastq {
         File read1 = outputRead1
         File? read2 = outputRead2
         File? read0 = outputRead0
+        File? readS = outputReadS
     }
 
     runtime {
@@ -217,6 +220,7 @@ task Fastq {
         outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
         outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
         outputRead0: {description: "The location the unpaired reads should be written to (in case of paired-end sequenicng).", category: "advanced"}
+        outputReadS: {description: "The location singleton reads should be written to.", category: "advanced"}
         appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`.", category: "advanced"}
         outputQuality: {description: "Equivalent to samtools fastq's `-O` flag.", category: "advanced"}
         includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`.", category: "advanced"}
@@ -608,6 +612,7 @@ task Split {
     command {
         set -e
         mkdir -p "~{outputPath}/rg/"
+
         samtools split \
             --output-fmt bam \
             --output-fmt-option level=~{compressionLevel} \