Merge.

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.

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 {

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 <<<

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 {

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"

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 {

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 "}

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 {