From bf7aba3c332a8dcabc87d22e1740049ed4bf7db4 Mon Sep 17 00:00:00 2001
From: davycats <davycats.dc@gmail.com>
Date: Fri, 7 Oct 2022 17:59:35 +0200
Subject: [PATCH] add fastp
---
fastp.wdl | 101 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 101 insertions(+)
create mode 100644 fastp.wdl
diff --git a/fastp.wdl b/fastp.wdl
new file mode 100644
index 0000000..8cf99d9
--- /dev/null
+++ b/fastp.wdl
@@ -0,0 +1,101 @@
+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
--
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