From 041721c1f49d981e18477ad208ecad3580fb9dbd Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 21 Sep 2020 16:10:57 +0200
Subject: [PATCH] Remove metrics file.
---
CHANGELOG.md | 2 ++
centrifuge.wdl | 3 ---
2 files changed, 2 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ce42941..b11e422 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ Centrifuge: Remove metrics file from classification (which causes the
+ summary report to be empty). https://github.com/DaehwanKimLab/centrifuge/issues/83
+ Add NanoPlot and NanoQC tasks.
+ Centrifuge: Add `timeMinutes` to `Classify` task and remove unnecessary
downloading tasks (alternative is refseqtools).
diff --git a/centrifuge.wdl b/centrifuge.wdl
index bc2ea46..1e7a0b4 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -128,7 +128,6 @@ task Classify {
~{inputFormatOptions[inputFormat]} \
~{true="--phred64" false="--phred33" phred64} \
--min-hitlen ~{minHitLength} \
- ~{"--met-file " + outputPrefix + "_alignment_metrics.tsv"} \
--threads ~{threads} \
~{"--trim5 " + trim5} \
~{"--trim3 " + trim3} \
@@ -143,7 +142,6 @@ task Classify {
>>>
output {
- File metrics = outputPrefix + "_alignment_metrics.tsv"
File classification = outputPrefix + "_classification.tsv"
File report = outputPrefix + "_output_report.tsv"
}
@@ -175,7 +173,6 @@ task Classify {
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
- metrics: {description: "File with centrifuge metrics."}
classification: {description: "File with the classification results."}
report: {description: "File with a classification summary."}
}
--
GitLab