Commit a095517d authored by Boom's avatar Boom
Browse files

Update tool versions.

parent 84365831
......@@ -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.
......
......@@ -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 {
......
......@@ -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 <<<
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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"}
......
......@@ -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 {
......
......@@ -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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