From 1ad000b1370898459d2ef3d6e2b3939699874c4f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 13 Jan 2023 17:07:32 +0100
Subject: [PATCH] update samtools containers
---
samtools.wdl | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index 8503777..303f982 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -72,7 +72,7 @@ task DictAndFaidx {
String javaXmx = "2G"
String memory = "3GiB"
Int timeMinutes = 5 + ceil(size(inputFile, "GiB") * 5)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
String outputFile = basename(inputFile)
@@ -119,7 +119,7 @@ task Faidx {
String outputDir
String memory = "2GiB"
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
command {
@@ -168,7 +168,7 @@ task Fastq {
Int threads = 1
String memory = "1GiB"
Int timeMinutes = 1 + ceil(size(inputBam) * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
command {
@@ -232,7 +232,7 @@ task FilterShortReadsBam {
String memory = "1GiB"
Int timeMinutes = 1 + ceil(size(bamFile, "GiB") * 8)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
@@ -278,7 +278,7 @@ task Flagstat {
String memory = "256MiB" # Only 40.5 MiB used for 150G bam file.
Int timeMinutes = 1 + ceil(size(inputBam, "G"))
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
command {
@@ -318,7 +318,7 @@ task Index {
String memory = "2GiB"
Int timeMinutes = 1 + ceil(size(bamFile, "GiB") * 4)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
# Select_first is needed, otherwise womtool validate fails.
@@ -369,7 +369,7 @@ task Markdup {
String outputBamPath
Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
command {
@@ -408,7 +408,7 @@ task Merge {
Int threads = 1
String memory = "4GiB"
Int timeMinutes = 1 + ceil(size(bamFiles, "GiB") * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
String indexPath = sub(outputBamPath, "\.bam$",".bai")
@@ -463,7 +463,7 @@ task Sort {
Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb
Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
# Select first needed as outputPath is optional input (bug in cromwell).
@@ -576,7 +576,7 @@ task View {
Int threads = 1
String memory = "1GiB"
Int timeMinutes = 1 + ceil(size(inFile, "GiB") * 5)
- String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
+ String dockerImage = "quay.io/biocontainers/samtools:1.16.1--h6899075_1"
}
String outputIndexPath = basename(outputFileName) + ".bai"
--
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