From 2e1c9972b01922cd915b7041b230e6287dda778b Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 14 Nov 2022 13:40:06 +0100
Subject: [PATCH] fix issue where fastp errors if split is set to 1
---
fastp.wdl | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/fastp.wdl b/fastp.wdl
index 7f269d8..db4a2d4 100644
--- a/fastp.wdl
+++ b/fastp.wdl
@@ -41,11 +41,15 @@ task Fastp {
String memory = "50GiB"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 6.0 / threads)
String dockerImage = "quay.io/biocontainers/fastp:0.23.2--h5f740d0_3"
+
+ Int? noneInt
}
String outputDirR1 = sub(outputPathR1, basename(outputPathR1), "")
String outputDirR2 = sub(outputPathR2, basename(outputPathR2), "")
+ Int? effectiveSplit = if select_first([split, 1]) > 1 then split else noneInt
+
command <<<
set -e
mkdir -p $(dirname ~{outputPathR1})
@@ -54,8 +58,8 @@ task Fastp {
mkdir -p $(dirname ~{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
+ seq 1 ~{if defined(effectiveSplit) then effectiveSplit else "2"} | awk '{print "~{outputDirR1}/"$0".~{basename(outputPathR1)}"}' > r1_paths
+ seq 1 ~{if defined(effectiveSplit) then effectiveSplit else "2"} | awk '{print "~{outputDirR2}/"$0".~{basename(outputPathR2)}"}' > r2_paths
fastp \
-i ~{read1} \
~{"-I " + read2} \
@@ -66,21 +70,21 @@ task Fastp {
-z ~{compressionLevel} \
~{if correction then "--correction" else ""} \
--length_required ~{lengthRequired} \
- --thread ~{select_first([split, threads])} \
- ~{"--split " + split} \
- ~{if defined(split) then "-d 0" else ""} \
+ --thread ~{select_first([effectiveSplit, threads])} \
+ ~{"--split " + effectiveSplit} \
+ ~{if defined(effectiveSplit) then "-d 0" else ""} \
~{if performAdapterTrimming then "" else "--disable_adapter_trimming"}
>>>
output {
File htmlReport = htmlPath
File jsonReport = jsonPath
- Array[File] clippedR1 = if defined(split) then read_lines("r1_paths") else [outputPathR1]
- Array[File] clippedR2 = if defined(split) then read_lines("r2_paths") else [outputPathR2]
+ Array[File] clippedR1 = if defined(effectiveSplit) then read_lines("r1_paths") else [outputPathR1]
+ Array[File] clippedR2 = if defined(effectiveSplit) then read_lines("r2_paths") else [outputPathR2]
}
runtime {
- cpu: select_first([split, threads])
+ cpu: select_first([effectiveSplit, threads])
memory: memory
time_minutes: timeMinutes
docker: dockerImage
--
GitLab