add fastp

fastp.wdl

+verison 1.0
+
+# MIT License
+#
+# Copyright (c) 2022 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 Fastp {
+    input {
+        File r1
+        File r2
+        String outputPathR1
+        String outputPathR2
+        String htmlPath
+        String jsonPath
+
+        Int compressionLevel = 1
+        Boolean correction = false
+        Int lengthRequired = 15
+        Int? split
+        
+        Int threads = 4
+        String memory = "5GiB"
+        Int timeMinutes = 1 + ceil(size([read1, read2], "G")  * 7.0 / cores)
+        String dockerImage = "quay.io/biocontainers/fastp:0.23.2--h5f740d0_3"
+    }
+
+    String outputDirR1 = sub(outputPathR1, basename(outputPathR1), "")
+
+    command {
+        set -e 
+        mkdir -p $(dirname ~{outputPathR1} ~{outputPathR2} ~{htmlPath} ~{jsonPath})
+        # predict output paths
+        seq 1 ~{if defined(split) then split else "2"} | awk '{print "~{outputDirR1}/"$0".~{basename(outputPathR1)}"}' > r1_paths
+        seq 1 ~{if defined(split) then split else "2"} | awk '{print "~{outputDirR2}/"$0".~{basename(outputPathR2)}"}' > r2_paths
+        fastp \
+        -i ~{r1} \
+        ~{"-I " + r2} \
+        -o ~{outputPathR1} \
+        ~{"-O " + outputPathR2} \
+        -h ~{htmlPath} \
+        -j ~{jsonPath} \
+        -z ~{compressionLevel} \
+        ~{if correction then "--correction" else ""} \
+        --length_required ~{lengthRequired} \
+        --threads ~{threads} \
+        ~{"--split " + split} \
+        ~{if defined(split) then "-d 0" else ""}
+    }
+
+    Array[String] r1Paths = read_lines("r1_paths")
+    Array[String] r2Paths = read_lines("r2_paths")
+
+    output {
+        File htmlReport = htmlPath
+        File jsonReport = jsonPath
+        Array[File] clippedR1 = if defined(split) then r1Paths else [outputPathR1]
+        Array[File] clippedR2 = if defined(split) then r2Paths else [outputPathR2]
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        r1: {description: "The R1 fastq file.", category: "required"}
+        r2: {description: "The R2 fastq file.", category: "required"}
+        outputPathR1: {description: "The output path for the R1 file.", category: "required"}
+        outputPathR2: {description: "The output path for the R2 file.", category: "required"}
+        htmlPath: {description: "The path to write the html report to.", category: "required"}
+        jsonPath: {description: "The path to write the json report to.", category: "required"}
+        compressionLevel: {description: "The compression level to use for the output.", category: "advanced"}
+        correction: {description: "Whether or not to apply overlap based correction.", category: "advanced"}
+        lengthRequired: {description: "The minimum read length.", category: "advanced"}
+        split: {description: "The number of chunks to split the files into.", category: "common"}
+        threads: {description: "The number of threads to use.", 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"}
+    }
+}
\ No newline at end of file