diff --git a/CHANGELOG.md b/CHANGELOG.md
index c4eb9ac56cdfd6efbcc709f915f3b4f356ddd06d..f4bade6634b18e06b75e4bf29e891a9685196a4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,16 +10,23 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+<<<<<<< HEAD
+ Fix output files in ccs.wdl.
++ 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 2ae22a57acfdd005cd048255e67e85b5c3d294ce..0bdccca8db6abfcc9ae3b99c721796a7f0b1af4f 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 06b1d75696989151b61360883b94fba7c4114528..dead830383705ee298c2bb018142915bca494b03 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/common.wdl b/common.wdl
index 66bdb99cf645a36fc83192c999524c86998e26b3..54b11567e8c778ba0563d32095a43490603fa26d 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 2455aaac1934d6303bf0ea2b25bf85093f8f7b4f..6b87ad4f3120baa2e1e3f13d5f9f1d223419bb80 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"}
@@ -91,13 +91,13 @@ task Lima {
dirName="$(dirname ~{outputPrefix})"
find "$(cd ${dirName}; pwd)" -name "*.bam" > bamFiles.txt
find "$(cd ${dirName}; pwd)" -name "*.bam.pbi" > bamIndexes.txt
- find "$(cd ${dirName}; pwd)" -name "*.subreadset.xml" > subreadsets.txt
+ find "$(cd ${dirName}; pwd)" -name "*.consensusreadset.xml" > consensusreadset.txt
>>>
output {
Array[File] limaBam = read_lines("bamFiles.txt")
Array[File] limaBamIndex = read_lines("bamIndexes.txt")
- Array[File] limaXml = read_lines("subreadsets.txt")
+ Array[File] limaXml = read_lines("consensusreadset.txt")
File limaStderr = outputPrefix + ".lima.stderr.log"
File limaJson = outputPrefix + ".json"
File limaCounts = outputPrefix + ".lima.counts"
diff --git a/minimap2.wdl b/minimap2.wdl
index d2e699052d89b9dc19ce6806ed1f68524593be78..50ff4db38525cc8e896c944e5bc8de64e52f8a0f 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 f86641b0613e207f7633cde189b8be0415515a38..e4c94a43b113f35c6ae82c228711bd8ce4592490 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 "}
diff --git a/pacbio.wdl b/pacbio.wdl
index 7c0113fd5c6188dcebdee7c53ab0489d3200a4aa..b21c69bc0b3db02ed0e1b3ea5fc46fb9bebe4ed4 100644
--- a/pacbio.wdl
+++ b/pacbio.wdl
@@ -26,7 +26,7 @@ task mergePacBio {
String outputPathMergedReport
String memory = "4G"
- String dockerImage = "lumc/pacbio-merge:0.2"
+ String dockerImage = "quay.io/redmar_van_den_berg/pacbio-merge:0.2"
}
command {