From 39cbad542c2c306714ef434a1942107a6377e42b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:24:28 +0200
Subject: [PATCH] fastqc to 1.0
---
fastqc.wdl | 81 +++++++++++++++++++++++++++++-------------------------
1 file changed, 43 insertions(+), 38 deletions(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index d9135f7..a11e1bf 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -1,20 +1,24 @@
+version 1.0
+
task fastqc {
- File seqFile
- String outdirPath
- String? preCommand
- Boolean? casava
- Boolean? nano
- Boolean? noFilter
- Boolean? extract = true
- Boolean? nogroup
- Int? minLength
- String? format
- Int? threads = 1
- File? contaminants
- File? adapters
- File? limits
- Int? kmers
- String? dir
+ input {
+ File seqFile
+ String outdirPath
+ String? preCommand
+ Boolean? casava
+ Boolean? nano
+ Boolean? noFilter
+ Boolean? extract = true
+ Boolean? nogroup
+ Int? minLength
+ String? format
+ Int? threads = 1
+ File? contaminants
+ File? adapters
+ File? limits
+ Int? kmers
+ String? dir
+ }
# Chops of the .gz extension if present.
String name = sub(seqFile, "\\.gz$","")
# This regex chops of the extension and replaces it with _fastqc for the reportdir.
@@ -22,24 +26,24 @@ task fastqc {
String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p ${outdirPath}
+ ~{preCommand}
+ mkdir -p ~{outdirPath}
fastqc \
- ${"--outdir " + outdirPath} \
- ${true="--casava" false="" casava} \
- ${true="--nano" false="" nano} \
- ${true="--nofilter" false="" noFilter} \
- ${true="--extract" false="" extract} \
- ${true="--nogroup" false="" nogroup} \
- ${"--min_length " + minLength } \
- ${"--format " + format} \
- ${"--threads " + threads} \
- ${"--contaminants " + contaminants} \
- ${"--adapters " + adapters} \
- ${"--limits " + limits} \
- ${"--kmers " + kmers} \
- ${"--dir " + dir} \
- ${seqFile}
+ ~{"--outdir " + outdirPath} \
+ ~{true="--casava" false="" casava} \
+ ~{true="--nano" false="" nano} \
+ ~{true="--nofilter" false="" noFilter} \
+ ~{true="--extract" false="" extract} \
+ ~{true="--nogroup" false="" nogroup} \
+ ~{"--min_length " + minLength } \
+ ~{"--format " + format} \
+ ~{"--threads " + threads} \
+ ~{"--contaminants " + contaminants} \
+ ~{"--adapters " + adapters} \
+ ~{"--limits " + limits} \
+ ~{"--kmers " + kmers} \
+ ~{"--dir " + dir} \
+ ~{seqFile}
}
@@ -56,13 +60,14 @@ task fastqc {
}
task getConfiguration {
- String? preCommand
- String? fastqcDirFile = "fastqcDir.txt"
-
+ input {
+ String? preCommand
+ String? fastqcDirFile = "fastqcDir.txt"
+ }
command {
set -e -o pipefail
- ${preCommand}
- echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile}
+ ~{preCommand}
+ echo $(dirname $(readlink -f $(which fastqc))) > ~{fastqcDirFile}
}
output {
--
GitLab