From ab88bc1ac6feaf4002d5849acec90bb61d523fd0 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:33:46 +0200
Subject: [PATCH] mergecounts to 1.0
---
mergecounts.wdl | 33 ++++++++++++++++++---------------
1 file changed, 18 insertions(+), 15 deletions(-)
diff --git a/mergecounts.wdl b/mergecounts.wdl
index 8cca5dd..9d87740 100644
--- a/mergecounts.wdl
+++ b/mergecounts.wdl
@@ -1,26 +1,29 @@
-task MergeCounts {
- String? preCommand
-
- Array[File] inputFiles
- String outputFile
- Int featureColumn
- Int valueColumn
- Boolean inputHasHeader
+version 1.0
+task MergeCounts {
+ input {
+ String? preCommand
+
+ Array[File] inputFiles
+ String outputFile
+ Int featureColumn
+ Int valueColumn
+ Boolean inputHasHeader
+ }
# Based on a script by Szymon Kielbasa/Ioannis Moustakas
command <<<
set -e -o pipefail
- mkdir -p ${sub(outputFile, basename(outputFile) + "$", "")}
- ${preCommand}
+ mkdir -p ~{sub(outputFile, basename(outputFile) + "$", "")}
+ ~{preCommand}
R --no-save <<CODE
library(dplyr)
library(reshape2)
- listOfFiles <- c("${sep='", "' inputFiles}")
+ listOfFiles <- c("~{sep='", "' inputFiles}")
- valueI <- ${valueColumn}
- featureI <- ${featureColumn}
- header <- ${true="TRUE" false="FALSE" inputHasHeader}
+ valueI <- ~{valueColumn}
+ featureI <- ~{featureColumn}
+ header <- ~{true="TRUE" false="FALSE" inputHasHeader}
d <- do.call(rbind, lapply(listOfFiles, function(file){
d <- read.table(file, sep="\t", header=header, comment.char="#")
@@ -34,7 +37,7 @@ task MergeCounts {
}))
d <- d %>% dcast(feature ~ sample, value.var="count")
- write.table(d, file="${outputFile}", sep="\t", quote=FALSE, row.names=FALSE)
+ write.table(d, file="~{outputFile}", sep="\t", quote=FALSE, row.names=FALSE)
CODE
>>>
--
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