From 346c0044a15279e1e3c5cd7140e24d9321255be8 Mon Sep 17 00:00:00 2001
From: davycats <davycats.dc@gmail.com>
Date: Fri, 14 Oct 2022 15:21:07 +0200
Subject: [PATCH] fix fastp task
---
fastp.wdl | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/fastp.wdl b/fastp.wdl
index 3063d01..c7a4d19 100644
--- a/fastp.wdl
+++ b/fastp.wdl
@@ -48,7 +48,11 @@ task Fastp {
command <<<
set -e
- mkdir -p $(dirname ~{outputPathR1} ~{outputPathR2} ~{htmlPath} ~{jsonPath})
+ mkdir -p $(dirname ~{outputPathR1})
+ mkdir -p $(dirname ~{outputPathR2})
+ mkdir -p $(dirname ~{htmlPath})
+ 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
@@ -68,14 +72,11 @@ task Fastp {
~{if performAdapterTrimming then "" else "--disable_adapter_trimming"}
>>>
- 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]
+ 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]
}
runtime {
--
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