From 0eee972fecacd2bcff3a24c739cf89c3d9719c64 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 2 Jul 2019 07:23:14 +0200
Subject: [PATCH] dockerImage for gffread and CPAT
---
CPAT.wdl | 4 ++--
gffread.wdl | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/CPAT.wdl b/CPAT.wdl
index 0c4e83d..b92053d 100644
--- a/CPAT.wdl
+++ b/CPAT.wdl
@@ -11,7 +11,7 @@ task CPAT {
# CPAT should not index the reference genome.
Array[String]? startCodons
Array[String]? stopCodons
- String dockerTag = "v1.2.4_cv1"
+ String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
}
# Some WDL magic in the command section to properly output the start and stopcodons to the command.
@@ -34,7 +34,7 @@ task CPAT {
}
runtime {
- docker: "biocontainers/cpat:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/gffread.wdl b/gffread.wdl
index 08b2e8d..da99781 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -10,7 +10,7 @@ task GffRead {
String? proteinFastaPath
String? filteredGffPath
Boolean outputGtfFormat = false
- String dockerTag = "0.9.12--0"
+ String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
}
# The mkdirs below are hackish. It should be
@@ -41,6 +41,6 @@ task GffRead {
}
runtime {
- docker: "quay.io/biocontainers/gffread:" + dockerTag
+ docker: dockerImage
}
}
\ No newline at end of file
--
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