From a095517d6f9e729769e26e1bd7dd6385ac403fc1 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Thu, 10 Jun 2021 16:20:34 +0200
Subject: [PATCH] Update tool versions.
---
CHANGELOG.md | 18 ++++++++++++------
bam2fastx.wdl | 4 ++--
biowdl.wdl | 2 +-
ccs.wdl | 2 +-
common.wdl | 2 +-
lima.wdl | 2 +-
minimap2.wdl | 4 ++--
nanopack.wdl | 2 +-
8 files changed, 21 insertions(+), 15 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e47033c..9112c77 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,15 +10,21 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ Update biowdl-input-converter to version 0.3.
++ Update minimap2 to version 2.20.
++ Update lima to version 2.2.0.
++ Update ccs to version 6.0.0.
++ Update bam2fastx to version 1.3.1.
+ Add memory values to GffCompare, GffRead and CPAT.
+ GffCompare: Make the `referenceAnnotation` input optional.
+ Stringtie: Add the `minimumCoverage` input.
-+ UMI-tools: update default dockerImage to use umitools v1.1.1 with correct samtools version (1.10)
-+ UMI-tools: re-introduce samtools indexing
-+ UMI-tools: update default dockerImage to use umitools v1.1.1
-+ UMI-tools dedup: Add tempdir
-+ Update BCFTOOLS view: add options for filtering (include, exclude, excludeUncalled).
-+ Duphold: add duphold.wdl.
++ UMI-tools: Update default dockerImage to use umitools v1.1.1 with correct
+ samtools version (1.10).
++ UMI-tools: Re-introduce samtools indexing.
++ UMI-tools: Update default dockerImage to use umitools v1.1.1.
++ UMI-tools dedup: Add tempdir.
++ Bcftools view: Add options for filtering (include, exclude, excludeUncalled).
++ Duphold: Add `duphold.wdl`.
+ Add new wdl file prepareShiny.wdl for creating input files for shiny app.
+ mergePacBio: Rename `mergedReport` to `outputPathMergedReport`.
+ Lima: Fix copy commands.
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 2ae22a5..0bdccca 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -32,7 +32,7 @@ task Bam2Fasta {
String memory = "2G"
Int timeMinutes = 15
- String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.0--he1c1bb9_8"
+ String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
}
command {
@@ -100,7 +100,7 @@ task Bam2Fastq {
String memory = "2G"
Int timeMinutes = 15
- String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.0--he1c1bb9_8"
+ String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
}
command {
diff --git a/biowdl.wdl b/biowdl.wdl
index 06b1d75..dead830 100644
--- a/biowdl.wdl
+++ b/biowdl.wdl
@@ -34,7 +34,7 @@ task InputConverter {
String memory = "128M"
Int timeMinutes = 1
- String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
+ String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.3.0--pyhdfd78af_0"
}
command <<<
diff --git a/ccs.wdl b/ccs.wdl
index 4446937..69095f4 100644
--- a/ccs.wdl
+++ b/ccs.wdl
@@ -37,7 +37,7 @@ task CCS {
Int threads = 2
String memory = "4G"
Int timeMinutes = 1440
- String dockerImage = "quay.io/biocontainers/pbccs:5.0.0--0"
+ String dockerImage = "quay.io/biocontainers/pbccs:6.0.0--h9ee0642_2"
}
command {
diff --git a/common.wdl b/common.wdl
index 66bdb99..54b1156 100644
--- a/common.wdl
+++ b/common.wdl
@@ -221,7 +221,7 @@ task YamlToJson {
String memory = "128M"
Int timeMinutes = 1
# biowdl-input-converter has python and pyyaml.
- String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
+ String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.3.0--pyhdfd78af_0"
}
command {
diff --git a/lima.wdl b/lima.wdl
index 2455aaa..f6faf07 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -51,7 +51,7 @@ task Lima {
Int threads = 2
String memory = "2G"
Int timeMinutes = 30
- String dockerImage = "quay.io/biocontainers/lima:2.0.0--0"
+ String dockerImage = "quay.io/biocontainers/lima:2.2.0--h9ee0642_0"
}
Map[String, String] libraryDesignOptions = {"same": "--same", "different": "--different", "neighbors": "--neighbors"}
diff --git a/minimap2.wdl b/minimap2.wdl
index d2e6990..50ff4db 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -33,7 +33,7 @@ task Indexing {
Int cores = 1
String memory = "4G"
Int timeMinutes = 10
- String dockerImage = "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
+ String dockerImage = "quay.io/biocontainers/minimap2:2.20--h5bf99c6_0"
}
command {
@@ -100,7 +100,7 @@ task Mapping {
Int cores = 4
String memory = "30G"
Int timeMinutes = 1 + ceil(size(queryFile, "G") * 200 / cores)
- String dockerImage = "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
+ String dockerImage = "quay.io/biocontainers/minimap2:2.20--h5bf99c6_0"
}
command {
diff --git a/nanopack.wdl b/nanopack.wdl
index f86641b..e4c94a4 100644
--- a/nanopack.wdl
+++ b/nanopack.wdl
@@ -42,7 +42,7 @@ task NanoPlot {
Int threads = 2
String memory = "2G"
Int timeMinutes = 15
- String dockerImage = "quay.io/biocontainers/nanoplot:1.32.1--py_0"
+ String dockerImage = "quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0"
}
Map[String, String] fileTypeOptions = {"fastq": "--fastq ", "fasta": "--fasta ", "fastq_rich": "--fastq_rich ", "fastq_minimal": "--fastq_minimal ", "summary": "--summary ", "bam": "--bam ", "ubam": "--ubam ", "cram": "--cram ", "pickle": "--pickle ", "feather": "--feather "}
--
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