From c7f9302dedc36f2d8036ca4d0de06298c442979d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 21 Feb 2019 15:54:15 +0100
Subject: [PATCH] dockerify gffread
---
gffread.wdl | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/gffread.wdl b/gffread.wdl
index da65f5f..aebe301 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -2,7 +2,6 @@ version 1.0
task GffRead {
input {
- String? preCommand
File inputGff
File genomicSequence
File? genomicIndex # Optional. GFFRead can create this by itself.
@@ -11,6 +10,7 @@ task GffRead {
String? proteinFastaPath
String? filteredGffPath
Boolean outputGtfFormat = false
+ String dockerTag = "0.9.12--0"
}
# The mkdirs below are hackish. it should be
@@ -18,7 +18,6 @@ task GffRead {
# but this goes wrong. Cromwell will always use ')' even if somepath is not defined. Which leads to crashing.
command {
set -e -o pipefail
- ~{preCommand}
~{"mkdir -p $(dirname " + CDSFastaPath}~{true=")" false="" defined(CDSFastaPath)}
~{"mkdir -p $(dirname " + exonsFastaPath}~{true=")" false="" defined(exonsFastaPath)}
~{"mkdir -p $(dirname " + proteinFastaPath}~{true=")" false="" defined(proteinFastaPath)}
@@ -26,11 +25,11 @@ task GffRead {
gffread \
~{inputGff} \
-g ~{genomicSequence} \
- ${"-w " + exonsFastaPath} \
- ${"-x " + CDSFastaPath} \
- ${"-y " + proteinFastaPath} \
- ${"-o " + filteredGffPath} \
- ${true="-T " false="" outputGtfFormat}
+ ~{"-w " + exonsFastaPath} \
+ ~{"-x " + CDSFastaPath} \
+ ~{"-y " + proteinFastaPath} \
+ ~{"-o " + filteredGffPath} \
+ ~{true="-T " false="" outputGtfFormat}
}
output {
@@ -39,4 +38,8 @@ task GffRead {
File? proteinFasta = proteinFastaPath
File? filteredGff = filteredGffPath
}
+
+ runtime {
+ docker: "quay.io/biocontainers/gffread:" + dockerTag
+ }
}
\ No newline at end of file
--
GitLab