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CHANGELOG.md

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Changelog

version develop

  • Replace bam2fastx task with samtools fastq task.
  • Update samtools to version 1.12.
  • Change pacbio-merge from dockerhub to quay.
  • Update multiqc to version 1.10.
  • Update biowdl-input-converter to version 0.3.
  • Update lima to version 2.2.0.
  • Update ccs to version 6.0.0.
  • Update bam2fastx to version 1.3.1.
  • Add the dockerImages to the output section.
  • Replace travis with github CI.
  • Reinstate outputDirectory input.
  • Move tasks ccsChunks & mergePacBio to tasks repository.
  • Update IsoSeq3 to version 3.4.0, Lima to version 2.0.0.
  • The pipeline now only supports a single input subreads bamfile and barcodes fasta file.
  • Rename main pipeline file to pacbio-subreads-processing.wdl.
  • Remove YAML file with docker images and set defaults within pacbio-subreads-processing.wdl inputs.
  • Make CPU cores for ccs configurable.
  • Add bam to fastq tasks to the pipeline.
  • Make CPU cores for lima configurable.
  • Update tasks and the input/output names.
  • Rename workflow outputs to shorter names.
  • Add multiqc to the pipeline.
  • Add meta {allowNestedInputs: true} to the workflows, to allow for the use of nested inputs.
  • Remove execute from the naming structure for calls of tasks and workflows.
  • Add sample names to workflow output as outputSamples.
  • Rename fastqc tasks to correctly reflect what input they process.
  • Rename test files to show pacbio file structure more clearly.
  • Increase the number of fastqc threads. This prevents java heapspace memory errors.
  • Make running isoseq3 refine optional. This changes the default behaviour to not running isoseq3 refine.
  • Add fastqc to the pipeline.
  • Tasks were updated to contain the time_minutes runtime attribute and associated timeMinutes input, describing the maximum time the task will take to run.
  • Setup pacbio subreads processing pipeline.