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@cagaser cagaser released this 08 Jul 13:51
· 350 commits to master since this release
v5.0.0
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version 5.0.0

  • Update CPAT to version 3.0.4.
    • Changed the outFilePath input to outputPrefix.
  • Survivor: Change integer to string literal in boolean parameters.
  • Samtools: Add mkdir line to Fastq task.
  • Add new parameters from CCS version 6.0.0 and add two new outputs:
    ccs_report.txt & zmw_metrics.json.gz.
  • Change CutAdapt memory to 5G.
  • Increase multiqc base time from 5 to 10.
  • 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.
  • 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.
  • Fixed the size call in the default for gffread's timeMinutes, to retrieve
    GBs instead of bytes.
  • Update stringtie to version 1.3.6.
  • 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 StringTie to version 2.1.4.
  • Complete parameter_meta for tasks missing the outputs.
  • DeepVariant: Add an optional input for the gvcf index.
  • Samtools: Sort task now has threads in runtime instead of 1.
  • Picard: Add parameter_meta to SortSam.
  • pbmm2: Add parameter_meta for sample.
  • Centrifuge: Rename output in task KReport to KrakenReport to resolve
    name collision with task name.
  • Bwa & bwa-mem2: Add parameter_meta for outputHla.
  • Multiqc: Removed WDL_AID excludes of "finished" & "dependencies" inputs.
  • Bam2fastx: Add localisation of input files to Bam2Fasta task.
  • Lima: cores input has been renamed to threads to match tool naming.
  • isoseq3: cores input has been renamed to threads to match tool naming.
  • CCS: cores input has been renamed to threads to match tool naming.
  • Add PacBio preprocessing specific tasks mergePacBio & ccsChunks.
  • CCS: Update CCS to version 5.
  • deepvariant: Add task for DeepVariant.
  • gatk: Make intervals optional for GenotypeGVCFs.
  • isoseq3: Add required bam index input to isoseq3.
  • pbbam: Add task for indexing PacBio bam files.
  • picard: Add CollectHsMetrics and CollectVariantCallingMetrics.
  • Samtools: Add threads to parameter meta for Merge task.
  • bcftools: add tmpDir input to specify temporary directory when sorting.
  • bcftools: remove outputType and implement indexing based on output
    file extension.
  • NanoPack: Add parameter_meta to NanoPlot task.
  • Centrifuge: Remove metrics file from classification (which causes the
    summary report to be empty).
    DaehwanKimLab/centrifuge#83
  • Add NanoPlot and NanoQC tasks.
  • Centrifuge: Add timeMinutes to Classify task and remove unnecessary
    downloading tasks (alternative is refseqtools).
  • collect-columns: updated docker image to version 1.0.0 and added the
    sumOnDuplicateId input (defaults to false).
  • survivor: replace integer boolean type to logical true or false value.
  • vt: Add option to ignore masked reference.
  • bcftools: add sorting and annotation.
  • Bam2fastx: Input bam and index are now arrays.
  • Lima: Remove globs from outputs.
  • Updated task gridss.wdl: add --jvmheap parameter.
  • A bwa-mem2 task was created with the same interface (including usePostalt)
    as the bwa mem task.
  • bwa mem and bwa kit are now one task. The usePostalt boolean can be used to
    switch the postalt script on and off.
  • Added a task for GRIDSS.
  • Add wdl file for pacbio's bam2fastx tool.
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