From a8a6af815f817c96017a47c24e3fc986e4ba97f8 Mon Sep 17 00:00:00 2001
From: npappas <N.Pappas@lumc.nl>
Date: Fri, 11 May 2018 13:45:04 +0200
Subject: [PATCH] Update centrifuge command and add kreport task
---
centrifuge.wdl | 52 ++++++++++++++++++++++++++++++++++++++++++++------
1 file changed, 46 insertions(+), 6 deletions(-)
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 69e5de7..740ef50 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -56,14 +56,16 @@ task build {
task classify {
String outputDir
+ Boolean compressOutput = true
String? preCommand
String indexPrefix
File? unpairedReads
File read1
File? read2
Boolean? fastaInput
- String? outputFile = outputDir + "/centrifuge.out"
- String? reportFile = outputDir + "/centrifuge_report.tsv"
+ String? outputFilePath = outputDir + "/centrifuge.out"
+ String? reportFilePath = outputDir + "/centrifuge_report.tsv"
+ String? metFilePath # If this is specified, the report file is empty
Int? assignments
Int? minHitLen
Int? minTotalLen
@@ -84,17 +86,17 @@ task classify {
${true="-1 " false="-U " defined(read2)} ${read1} \
${"-2 " + read2} \
${"-U " + unpairedReads} \
- ${"--report-file " + reportFile} \
+ ${"--report-file " + reportFilePath} \
${"--min-hitlen " + minHitLen} \
${"--min-totallen " + minTotalLen} \
${true="--host-taxids " false="" defined(hostTaxIds)} ${sep=',' hostTaxIds} \
${true="--exclude-taxids " false="" defined(excludeTaxIds)} ${sep=',' excludeTaxIds} \
- ${"-S " + outputFile}
+ ${true="| gzip -c > " false="-S " compressOutput}${outputFilePath}${true=".gz" false="" compressOutput}
}
output {
- File outFile = select_first([outputFile])
- File reportFile = select_first([reportFile])
+ File classifiedReads = if (compressOutput) then select_first([outputFilePath + ".gz"]) else select_first([outputFilePath])
+ File reportFile = select_first([reportFilePath])
}
runtime {
@@ -163,3 +165,41 @@ task downloadTaxonomy {
}
}
+task kreport {
+ String? preCommand
+ String outputDir
+ File centrifugeOut
+ Boolean inputIsCompressed
+ String kreportPath=sub(centrifugeOut, "\\.out.*", "\\.kreport")
+ String indexPrefix
+ Boolean? onlyUnique
+ Boolean? showZeros
+ Boolean? isCountTable
+ Int? minScore
+ Int? minLength
+ Int? cores
+ Int? memory
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ centrifuge-kreport \
+ -x ${indexPrefix} \
+ ${true="--only-unique" false="" onlyUnique} \
+ ${true="show-zeros" false="" showZeros} \
+ ${true="--is-count-table" false="" isCountTable} \
+ ${"--min-score " + minScore} \
+ ${"--min-length " + minLength} \
+ ${true="<(zcat " false="" inputIsCompressed}${centrifugeOut}${true=")" false="" inputIsCompressed} \
+ > ${kreportPath}
+ }
+
+ output {
+ File kreport = select_first([kreportPath])
+ }
+
+ runtime {
+ cpu: select_first([cores, 1])
+ memory: select_first([memory, 4])
+ }
+}
--
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