From 46d05bb5fc546840bcd2c4751b99dc4fa137aa69 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 10 Dec 2019 17:02:49 +0100
Subject: [PATCH] Update TALON output to align with new version.
---
CHANGELOG.md | 2 ++
common.wdl | 2 +-
talon.wdl | 19 +++++++++----------
3 files changed, 12 insertions(+), 11 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 09418cc..ebe58ea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 2.2.0-dev
---------------------------
++ Update biowdl-input-converter in common.wdl to version 0.2.1.
++ Update TALON section to now include the new annotation file.
+ Update TALON default image to version 4.4.1.
version 2.1.0
diff --git a/common.wdl b/common.wdl
index dccac85..21227e4 100644
--- a/common.wdl
+++ b/common.wdl
@@ -162,7 +162,7 @@ task YamlToJson {
File yaml
String outputJson = basename(yaml, "\.ya?ml$") + ".json"
# biowdl-input-converter has python and pyyaml.
- String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.0--py_0"
+ String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
}
command {
set -e
diff --git a/talon.wdl b/talon.wdl
index 9c426e5..e350d13 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -446,7 +446,6 @@ task SummarizeDatasets {
task Talon {
input {
- File SAMfile
File configFile
File databaseFile
String genomeBuild
@@ -454,10 +453,9 @@ task Talon {
Int minimumIdentity = 0
String outputPrefix
String configFileName = basename(configFile)
- String SAMfileName = basename(SAMfile)
Int cores = 4
- String memory = "20G"
+ String memory = "25G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
@@ -465,7 +463,7 @@ task Talon {
set -e
mkdir -p $(dirname ~{outputPrefix})
mv ${configFile} ./${configFileName}
- mv ${SAMfile} ./${SAMfileName}
+ export TMPDIR=/tmp
talon \
~{"--f " + configFileName} \
~{"--db " + databaseFile} \
@@ -473,12 +471,13 @@ task Talon {
~{"--threads " + cores} \
~{"--cov " + minimumCoverage} \
~{"--identity " + minimumIdentity} \
- ~{"--o " + outputPrefix}
+ ~{"--o " + outputPrefix + "/run"}
}
output {
File outputUpdatedDatabase = databaseFile
- File outputLog = outputPrefix + "_talon_QC.log"
+ File outputLog = outputPrefix + "/run_QC.log"
+ File outputAnnot = outputPrefix + "/run_talon_read_annot.tsv"
}
runtime {
@@ -488,10 +487,6 @@ task Talon {
}
parameter_meta {
- SAMfile: {
- description: "Input SAM file, same one as described in configFile.",
- category: "required"
- }
configFile: {
description: "Dataset config file (comma-delimited).",
category: "required"
@@ -524,5 +519,9 @@ task Talon {
description: "Log file from TALON run.",
category: "required"
}
+ outputAnnot: {
+ description: "Read annotation file from TALON run.",
+ category: "required"
+ }
}
}
--
GitLab