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Commit 70b34844 authored by JasperBoom's avatar JasperBoom
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Update versions.

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CHANGELOG.md
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......@@ -10,6 +10,10 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+ Update Lima to version 2.0.0.
+ Update IsoSeq3 to version 3.4.0.
+ Update samtools to version 1.11.
+ Update Picard to version 2.23.8.
+ Update NanoPlot to version 1.32.1.
+ Update MultiQC to version 1.9.
+ Update CutAdapt to version 3.0.0.
......
isoseq3.wdl
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− 1
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......@@ -34,7 +34,7 @@ task Refine {
Int threads = 2
String memory = "2G"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
String dockerImage = "quay.io/biocontainers/isoseq3:3.4.0--0"
}
command {
......
lima.wdl
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......@@ -51,7 +51,7 @@ task Lima {
Int threads = 2
String memory = "2G"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
String dockerImage = "quay.io/biocontainers/lima:2.0.0--0"
}
Map[String, String] libraryDesignOptions = {"same": "--same", "different": "--different", "neighbors": "--neighbors"}
......
picard.wdl
+ 16
− 16
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......@@ -29,7 +29,7 @@ task BedToIntervalList {
String javaXmx = "3G"
String memory = "4G"
Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -89,7 +89,7 @@ task CollectHsMetrics {
# Additional * 2 because picard multiple metrics reads the
# reference fasta twice.
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -158,7 +158,7 @@ task CollectMultipleMetrics {
Int memoryMb = javaXmxMb + 512
# Additional * 2 because picard multiple metrics reads the reference fasta twice.
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -284,7 +284,7 @@ task CollectRnaSeqMetrics {
String memory = "9G"
# With 6 minutes per G there were several timeouts.
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 12)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -342,7 +342,7 @@ task CollectTargetedPcrMetrics {
String javaXmx = "3G"
String memory = "4G"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -404,7 +404,7 @@ task CollectVariantCallingMetrics {
String javaXmx = "8G"
String memory = "9G"
Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -453,7 +453,7 @@ task CreateSequenceDictionary {
String javaXmx = "2G"
String memory = "3G"
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -503,7 +503,7 @@ task GatherBamFiles {
Int memoryMb = javaXmxMb + 512
# One minute per input gigabyte.
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 1)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -558,7 +558,7 @@ task GatherVcfs {
String javaXmx = "4G"
String memory = "5G"
Int timeMinutes = 1 + ceil(size(inputVcfs, "G") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -622,7 +622,7 @@ task MarkDuplicates {
String memoryMb = javaXmxMb + 512
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
# Task is assuming query-sorted input so that the Secondary and Supplementary reads get
......@@ -701,7 +701,7 @@ task MergeVCFs {
String javaXmx = "4G"
String memory = "5G"
Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
# Using MergeVcfs instead of GatherVcfs so we can create indices.
......@@ -757,7 +757,7 @@ task SamToFastq {
String javaXmx = "16G" # High memory default to avoid crashes.
String memory = "17G"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
File? noneFile
}
......@@ -818,7 +818,7 @@ task ScatterIntervalList {
String javaXmx = "3G"
String memory = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -859,7 +859,7 @@ task SortSam {
# GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778
Int XmxGb = ceil(maxRecordsInRam / 125001.0)
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......@@ -917,7 +917,7 @@ task SortVcf {
String javaXmx = "8G"
String memory = "9G"
Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
......@@ -967,7 +967,7 @@ task RenameSample {
String javaXmx = "8G"
String memory = "9G"
Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
}
command {
......
samtools.wdl
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......@@ -69,7 +69,7 @@ task Faidx {
String outputDir
String memory = "2G"
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
command {
......@@ -118,7 +118,7 @@ task Fastq {
Int threads = 1
String memory = "1G"
Int timeMinutes = 1 + ceil(size(inputBam) * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
command {
......@@ -180,7 +180,7 @@ task FilterShortReadsBam {
String memory = "1G"
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
......@@ -226,7 +226,7 @@ task Flagstat {
String memory = "256M" # Only 40.5 MiB used for 150G bam file.
Int timeMinutes = 1 + ceil(size(inputBam, "G"))
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
command {
......@@ -266,7 +266,7 @@ task Index {
String memory = "2G"
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
# Select_first is needed, otherwise womtool validate fails.
......@@ -317,7 +317,7 @@ task Markdup {
String outputBamPath
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
command {
......@@ -356,7 +356,7 @@ task Merge {
Int threads = 1
String memory = "4G"
Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
String indexPath = sub(outputBamPath, "\.bam$",".bai")
......@@ -411,7 +411,7 @@ task Sort {
Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
# Select first needed as outputPath is optional input (bug in cromwell).
......@@ -523,7 +523,7 @@ task View {
Int threads = 1
String memory = "1G"
Int timeMinutes = 1 + ceil(size(inFile, "G") * 5)
String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
}
String outputIndexPath = basename(outputFileName) + ".bai"
......
scripts @ 85e2ec54
Compare 0cca0f40...85e2ec54
Subproject commit 0cca0f40a8e9121e8dcc9e76838f85835a0d8e94
Subproject commit 85e2ec542b65be5f2a25c22db05c28700fbe6db5
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