From 57b7c80c4ce3734c91005ab904a0ceb660135b43 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 27 Jan 2020 16:48:03 +0100
Subject: [PATCH] Fix issue where centrifuge would fail on incorrect paths.
---
centrifuge.wdl | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/centrifuge.wdl b/centrifuge.wdl
index b9eb762..5f24365 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -90,7 +90,6 @@ task Classify {
String indexPrefix
Array[File]+ read1
String outputPrefix
- String outputName = basename(outputPrefix)
Array[File] read2 = []
Int? trim5
@@ -113,7 +112,7 @@ task Classify {
~{inputFormatOptions[inputFormat]} \
~{true="--phred64" false="--phred33" phred64} \
~{"--min-hitlen " + minHitLength} \
- ~{"--met-file " + outputPrefix + "/" + outputName + "_alignment_metrics.tsv"} \
+ ~{"--met-file " + outputPrefix + "_alignment_metrics.tsv"} \
~{"--threads " + threads} \
~{"--trim5 " + trim5} \
~{"--trim3 " + trim3} \
@@ -123,14 +122,14 @@ task Classify {
~{"-x " + indexPrefix} \
~{true="-1" false="-U" length(read2) > 0} ~{sep="," read1} \
~{true="-2" false="" length(read2) > 0} ~{sep="," read2} \
- ~{"-S " + outputPrefix + "/" + outputName + "_classification.tsv"} \
- ~{"--report-file " + outputPrefix + "/" + outputName + "_output_report.tsv"}
+ ~{"-S " + outputPrefix + "_classification.tsv"} \
+ ~{"--report-file " + outputPrefix + "_output_report.tsv"}
}
output {
- File outputMetrics = outputPrefix + "/" + outputName + "_alignment_metrics.tsv"
- File outputClassification = outputPrefix + "/" + outputName + "_classification.tsv"
- File outputReport = outputPrefix + "/" + outputName + "_output_report.tsv"
+ File outputMetrics = outputPrefix + "_alignment_metrics.tsv"
+ File outputClassification = outputPrefix + "_classification.tsv"
+ File outputReport = outputPrefix + "_output_report.tsv"
}
runtime {
@@ -146,7 +145,6 @@ task Classify {
indexPrefix: {description: "The basename of the index for the reference genomes.", category: "required"}
read1: {description: "List of files containing mate 1s, or unpaired reads.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
- outputName: {description: "The base name of the outputPrefix.", category: "required"}
read2: {description: "List of files containing mate 2s.", category: "common"}
trim5: {description: "Trim <int> bases from 5' (left) end of each read before alignment.", category: "common"}
trim3: {description: "Trim <int> bases from 3' (right) end of each read before alignment.", category: "common"}
--
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