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Commit ff47f07c authored by JasperBoom's avatar JasperBoom
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Update lima.

parent 02f71e17
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......@@ -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.
......
......@@ -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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