From ff47f07c0657f717fbf2311b56cdd3ad3b23a7c2 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 30 Nov 2020 17:22:38 +0100
Subject: [PATCH] Update lima.
---
CHANGELOG.md | 2 ++
lima.wdl | 39 ++++++++++++++++-----------------------
2 files changed, 18 insertions(+), 23 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a6cc9bf..0130372 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,8 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ mergePacBio: Rename `mergedReport` to `outputPathMergedReport`.
++ Lima: Fix copy commands.
+ Update Lima to version 2.0.0.
+ Update IsoSeq3 to version 3.4.0.
+ Update samtools to version 1.11.
diff --git a/lima.wdl b/lima.wdl
index c06a9a7..90cd698 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -56,7 +56,7 @@ task Lima {
Map[String, String] libraryDesignOptions = {"same": "--same", "different": "--different", "neighbors": "--neighbors"}
- command {
+ command <<<
set -e
mkdir -p "$(dirname ~{outputPrefix})"
lima \
@@ -83,33 +83,26 @@ task Lima {
~{true="--peek-guess" false="" peekGuess} \
--log-level ~{logLevel} \
--num-threads ~{threads} \
- ~{"--log-file " + outputPrefix + ".stderr.log"} \
+ ~{"--log-file " + outputPrefix + ".fl.stderr.log"} \
~{inputBamFile} \
~{barcodeFile} \
- ~{outputPrefix + ".bam"}
+ ~{outputPrefix + ".fl.bam"}
- # Copy the files with the default filename to the folder specified in
- # outputPrefix.
- if [[ -f "~{outputPrefix}.json" ]]
- then
- echo "Log files already at output location."
- else
- cp "~{basename(outputPrefix)}.json" "~{outputPrefix}.json"
- cp "~{basename(outputPrefix)}.lima.counts" "~{outputPrefix}.lima.counts"
- cp "~{basename(outputPrefix)}.lima.report" "~{outputPrefix}.lima.report"
- cp "~{basename(outputPrefix)}.lima.summary" "~{outputPrefix}.lima.summary"
- fi
- }
+ dirName="$(dirname ~{outputPrefix})"
+ find "$(cd ${dirName}; pwd)" -name "*.fl.*.bam" > bamFiles.txt
+ find "$(cd ${dirName}; pwd)" -name "*.fl.*.bam.pbi" > bamIndexes.txt
+ find "$(cd ${dirName}; pwd)" -name "*.fl.*.subreadset.xml" > subreadsets.txt
+ >>>
output {
- Array[File] limaBam = glob("*.bam")
- Array[File] limaBamIndex = glob("*.bam.pbi")
- Array[File] limaXml = glob("*.subreadset.xml")
- File limaStderr = outputPrefix + ".stderr.log"
- File limaJson = outputPrefix + ".json"
- File limaCounts = outputPrefix + ".lima.counts"
- File limaReport = outputPrefix + ".lima.report"
- File limaSummary = outputPrefix + ".lima.summary"
+ Array[File] limaBam = read_lines("bamFiles.txt")
+ Array[File] limaBamIndex = read_lines("bamIndexes.txt")
+ Array[File] limaXml = read_lines("subreadsets.txt")
+ File limaStderr = outputPrefix + ".fl.stderr.log"
+ File limaJson = outputPrefix + ".fl.json"
+ File limaCounts = outputPrefix + ".fl.lima.counts"
+ File limaReport = outputPrefix + ".fl.lima.report"
+ File limaSummary = outputPrefix + ".fl.lima.summary"
}
runtime {
--
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