From 7db21a6481522746b0699c2756083d57326be164 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 27 Oct 2020 16:02:35 +0100
Subject: [PATCH] Add support for outputPrefix with or without folder
---
chunked-scatter.wdl | 3 +++
lima.wdl | 10 ++++++++++
2 files changed, 13 insertions(+)
diff --git a/chunked-scatter.wdl b/chunked-scatter.wdl
index b54a7d2..8895c2a 100644
--- a/chunked-scatter.wdl
+++ b/chunked-scatter.wdl
@@ -24,6 +24,7 @@ task ChunkedScatter {
input {
File inputFile
String prefix = "./scatter"
+ Boolean splitContigs = false
Int? chunkSize
Int? overlap
Int? minimumBasesPerFile
@@ -40,6 +41,7 @@ task ChunkedScatter {
~{"-c " + chunkSize} \
~{"-o " + overlap} \
~{"-m " + minimumBasesPerFile} \
+ ~{true="--split-contigs " false="" splitContigs} \
~{inputFile}
}
@@ -108,6 +110,7 @@ task ScatterRegions {
splitContigs: {description: "If set, contigs are allowed to be split up over multiple files.", category: "advanced"}
scatterSizeMillions: {description: "Over how many million base pairs should be scattered.", category: "common"}
scatterSize: {description: "Overrides scatterSizeMillions with a smaller value if set.", category: "advanced"}
+ splitContigs: {description: "Allow contigs to be split during scattering.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
diff --git a/lima.wdl b/lima.wdl
index 38cf2d6..7ef9d4a 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -58,6 +58,7 @@ task Lima {
command {
set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
lima \
~{libraryDesignOptions[libraryDesign]} \
~{true="--score-full-pass" false="" scoreFullPass} \
@@ -86,6 +87,15 @@ task Lima {
~{inputBamFile} \
~{barcodeFile} \
~{outputPrefix + ".bam"}
+
+ # copy the files with the default filename to the folder specified in
+ # outputPrefix.
+ if [ "~{basename(outputPrefix)}.json" != "~{outputPrefix}.json" ]; then
+ cp "~{basename(outputPrefix)}.json" "~{outputPrefix}.json"
+ cp "~{basename(outputPrefix)}.lima.counts" "~{outputPrefix}.lima.counts"
+ cp "~{basename(outputPrefix)}.lima.report" "~{outputPrefix}.lima.report"
+ cp "~{basename(outputPrefix)}.lima.summary" "~{outputPrefix}.lima.summary"
+ fi
}
output {
--
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