From 86a249825272f9bb4384f87057593047402a1a37 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 6 Dec 2021 15:36:36 +0100
Subject: [PATCH] Add sampleposition in array task
---
common.wdl | 37 +++++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/common.wdl b/common.wdl
index d29ed5d..fc8dc48 100644
--- a/common.wdl
+++ b/common.wdl
@@ -148,6 +148,43 @@ task CreateLink {
}
}
+task GetSamplePositionInArray {
+ input {
+ Array[String] sampleIds
+ String sample
+
+ # python:3.7-slim's sha256 digest. This image is based on debian buster.
+ String dockerImage = "python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
+ }
+
+ command <<<
+ python <<CODE
+ samples = ['~{sep="','" sampleIds}']
+ print(samples.index('~{sample}'))
+ CODE
+ >>>
+
+ output {
+ Int position = read_int(stdout())
+ }
+
+ runtime {
+ # 4 gigs of memory to be able to build the docker image in singularity.
+ memory: "4G"
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ sampleIds: {description: "A list of sample ids.", category: "required"}
+ sample: {description: "The sample for which the position is wanted.", category: "required"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ position: {description: ""}
+ }
+}
+
task MapMd5 {
input {
Map[String,String] map
--
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