From c9c2fc44154d2a79b629647401c93cdc23591cae Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:20:33 +0200
Subject: [PATCH] common to 1.0
---
common.wdl | 90 ++++++++++++++++++++++++++----------------------------
1 file changed, 43 insertions(+), 47 deletions(-)
diff --git a/common.wdl b/common.wdl
index 863421d..21b84b6 100644
--- a/common.wdl
+++ b/common.wdl
@@ -1,10 +1,13 @@
-task AppendToStringArray {
- Array[String] array
- String string
+version 1.0
+task AppendToStringArray {
+ input {
+ Array[String] array
+ String string
+ }
command {
- echo "${sep='\n' array}
- ${string}"
+ echo "~{sep='\n' array}
+ ~{string}"
}
output {
@@ -18,27 +21,29 @@ task AppendToStringArray {
# This task will fail if the MD5sum doesn't match the file.
task CheckFileMD5 {
- File file
- String MD5sum
-
+ input {
+ File file
+ String MD5sum
+ }
command {
set -e -o pipefail
- MD5SUM=$(md5sum ${file} | cut -d ' ' -f 1)
- [ $MD5SUM = ${MD5sum} ]
+ MD5SUM=$(md5sum ~{file} | cut -d ' ' -f 1)
+ [ $MD5SUM = ~{MD5sum} ]
}
}
task ConcatenateTextFiles {
- Array[File] fileList
- String combinedFilePath
- Boolean? unzip = false
- Boolean? zip = false
-
+ input {
+ Array[File] fileList
+ String combinedFilePath
+ Boolean? unzip = false
+ Boolean? zip = false
+ }
command {
set -e -o pipefail
- ${"mkdir -p $(dirname " + combinedFilePath + ")"}
- ${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
- ${true="| gzip -c" false="" zip} > ${combinedFilePath}
+ ~{"mkdir -p $(dirname " + combinedFilePath + ")"}
+ ~{true='zcat' false= 'cat' unzip} ~{sep=' ' fileList} \
+ ~{true="| gzip -c" false="" zip} > ~{combinedFilePath}
}
output {
@@ -53,11 +58,12 @@ task ConcatenateTextFiles {
task CreateLink {
# Making this of type File will create a link to the copy of the file in the execution
# folder, instead of the actual file.
- String inputFile
- String outputPath
-
+ input {
+ String inputFile
+ String outputPath
+ }
command {
- ln -sf ${inputFile} ${outputPath}
+ ln -sf ~{inputFile} ~{outputPath}
}
output {
@@ -65,29 +71,17 @@ task CreateLink {
}
}
-# inspired by https://gatkforums.broadinstitute.org/wdl/discussion/9616/is-there-a-way-to-flatten-arrays
-task FlattenStringArray {
- Array[Array[String]] arrayList
-
- command {
- for line in $(echo ${sep=', ' arrayList}) ; \
- do echo $line | tr -d '"[],' ; done
- }
-
- output {
- Array[String] flattenedArray = read_lines(stdout())
- }
-
- runtime {
- memory: 1
- }
-}
+# DEPRECATED. USE BUILT-IN FLATTEN FUNCTION
+# task FlattenStringArray {}
+# Commented out to let pipelines that depend on this fail.
task MapMd5 {
- Map[String,String] map
+ input {
+ Map[String,String] map
+ }
command {
- cat ${write_map(map)} | md5sum - | sed -e 's/ -//'
+ cat ~{write_map(map)} | md5sum - | sed -e 's/ -//'
}
output {
@@ -101,10 +95,11 @@ task MapMd5 {
task ObjectMd5 {
- Object the_object
-
+ input {
+ Object the_object
+ }
command {
- cat ${write_object(the_object)} | md5sum - | sed -e 's/ -//'
+ cat ~{write_object(the_object)} | md5sum - | sed -e 's/ -//'
}
output {
@@ -117,11 +112,12 @@ task ObjectMd5 {
}
task StringArrayMd5 {
- Array[String] stringArray
-
+ input {
+ Array[String] stringArray
+ }
command {
set -eu -o pipefail
- echo ${sep=',' stringArray} | md5sum - | sed -e 's/ -//'
+ echo ~{sep=',' stringArray} | md5sum - | sed -e 's/ -//'
}
output {
--
GitLab