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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[v1.4.1]

Changed

  • Reconciled workflow with wf-template v5.3.0.
  • Updated Dorado to v0.8.1

[v1.4.0]

Added

  • IGV configuration file with --ref --igv options and either --output_fmt bam or --output_fmt cram.
  • Support for gzipped reference genomes.
  • output_fmt selects the output format for basecalled and aligned files.

Changed

  • Updated Dorado to v0.8.0
  • Reconciled workflow with wf-template v5.2.6.
  • Do not emit the reference FASTA file.
  • Collapse redundant RG and PG header lines when emitting BAM or CRAM.

Fixed

  • Workflow starting with --duplex --barcode_kit, despite duplex not supporting barcoding.
  • Workflow crashing with --ref {{ reference }} --barcode_kit.
  • Aligned reads will no longer be trimmed when demuxing to preserve mapping information.
  • Workflow emits confusing warning about Bonito filtering when using Dorado.

Removed

  • fastq_only and output_bam options replaced by output_fmt.
    • --output_fmt fastq can be used to output unaligned FASTQ instead of unaligned CRAM.
    • --output_fmt bam can be used to output unaligned or aligned BAM instead of CRAM.

[v1.3.0]

Added

  • Modified base calling with --duplex.
  • APK 5.0.0 model.

Changed

[v1.2.2]

Changes

  • Bug fix for downstream workflows and --poly_a_config which does not affect normal workflow use.

[v1.2.1]

Added

  • Output channel for demuxed BAM files for downstream use.

[v1.2.0]

### Added

  • Support for dorado demux to demultiplex barcoded runs. Specify your --barcode_kit to activate demultiplexing.
  • Support for poly(a) tail length estimation with --poly_a_config. You can configure by providng a TOML file to --poly_a_config which is described in detail here

Changed

[v1.1.9]

Fixed

[v1.1.8]

Changed

[v1.1.7]

Fixed

  • Workflow accepting incompatible --fastq_only and --duplex options
  • Dynamically updated report in --watch_path mode.

[v1.1.6]

Fixed

  • qscore_filter inadvertently disabled in v1.1.5

[v1.1.5]

Changed

  • Minor update to default resource requests on dorado task.

Added

  • Experimental feature switch.

[v1.1.4]

Changed

[v1.1.3]

Changed

  • Bumped memory directives for intense tasks to reduce likelihood of job failure
  • Default to parallel GPU usage when using awsbatch profile

Removed

  • Runtime driver check in Dorado process, as this is no longer available in the Dorado image

[v1.1.2]

Changed

[v1.1.1]

Added

  • Reintroduced RNA002 models

[v1.1.0]

[Added]

  • --duplex basecalling converts FAST5 to POD5 automatically
    • Converted POD5 files are deleted by default, use --output_pod5 to output converted POD5 files to the workflow output directory.

Changed

[v1.0.1]

Fixed

  • Workflow crashes with fast5 input
  • Workflow fails early when trying to use FAST5 input with Dorado duplex

[v1.0.0]

Added

  • RNA004 models
  • R941 v3.3 5mCG 5hmCG models
  • Duplex calling with option --duplex
    • Note that duplex calling is not optimised for streaming basecalling with --watch_path and may lead to lower duplex yield.
    • Duplex basecalling is currently not compatible with modified basecalling.

Changed

  • Updated Dorado to v0.3.2 (see https://github.com/nanoporetech/dorado/releases/tag/v0.3.2)
  • Pascal architecture GPUs are now supported
  • Bumped minimum required Nextflow version to 23.04.2
  • Users no longer need to provide --basecaller_cfg custom and/or --remora_cfg custom to override models with --basecaller_model_path and/or --remora_model_path respectively.

Fixed

  • bamstats process very slow when output_bam has been selected

[v0.7.2]

Added

  • v4.2 5mC and 6mA modification models

Changed

  • Updated Dorado to v0.3.1
  • GPU tasks are limited to run in serial by default to avoid memory errors
    • Users in cluster and cloud environments where GPU devices are scheduled must use -profile discrete_gpus to parallelise GPU work
    • A warning will be printed if the workflow detects it is running non-local execution but the discrete_gpus profile is not enabled
    • Additional guidance on GPU support is provided in our Quickstart
  • Bumped minimum required Nextflow version to 22.10.8

[v0.7.1]

Fixed

  • Command not found on cram_cache step
  • Typo in report that refers to the workflow as "wf-basecalling-report"

[v0.7.0]

Changed

  • Updated Dorado to v0.3.0
  • BAM may be output instead of CRAM by providing --output_bam
  • --help message will list basecalling and modbasecalling models available for use with the workflow

Added

  • v4.2.0 models, which must be used for sequencing runs performed at new 5 kHz sampling rate
  • v4.1.0 models replace v4.0.0 models and must be used for sequencing runs performed at 4 kHz sampling rate

Removed

  • v4.0.0 models

Fixed

  • Custom models were previously rejected by the workflow as basecaller_cfg and remora_cfg are validated against a list of basecalling models installed in the Dorado container.
    • Users should now provide --basecaller_cfg custom and/or --remora_cfg custom to override models with --basecaller_model_path and/or --remora_model_path respectively.
    • Providing --basecaller_cfg custom or --remora_cfg custom without the corresponding --basecaller_model_path or --remora_model_path will result in an error.

[v0.6.0]

Added

  • Ability to watch the input path and process files as they become available in real time.

[v0.5.2]

Added

  • Configuration for running demo data in AWS

[v0.5.1]

Fixed

[v0.5.0]

Changed

  • Updated Dorado to v0.2.4
  • Updated to Oxford Nanopore Technologies PLC. Public License

Fixed

  • Dorado image correctly ships with CUDA runtime library

[v0.4.1]

Fixed

  • Input ref channel depleted after first alignment

[v0.4.0]

Changed

  • Reference is no longer required for basecalling
    • CRAM files with no alignments will be generated if --ref is not provided
    • FASTQ may be output instead of CRAM by providing --fastq_only
  • PG line for converting Dorado SAM output to uBAM is no longer written to output header
  • Work directory is automatically cleaned up on successful completion to remove large intermediate files
    • Override this by including cleanup = false in a custom Nextflow configuration file
  • Number of threads for merging is now configurable for advanced users

[v0.3.0]

Changed

  • Updated Dorado to v0.2.1
  • --basecaller_cfg and --remora_cfg are now validated against a list of models installed in the Dorado container

Fixed

  • Workflow no longer prints a confusing error when Dorado fails

[v0.2.0]

Added

  • --basecaller_args may be used to provide custom arguments to the basecalling process

Changed

  • Updated Dorado to v0.1.1
    • Latest models are now v4.0.0
  • Workflow prints a more helpful error when Dorado fails due to unknown model name

[v0.1.2]

Changed

  • Updated description in manifest

[v0.1.1]

Fixed

  • Default basecaller_basemod_threads value
  • Undefined colors variable

[v0.1.0]

Added

  • Workflow will now output pass and fail CRAM
    • Reads are separated into pass and fail based on their mean qscore as calculated by dorado
    • The threshold can be changed with --qscore_filter

Changed

  • Improved --help documentation

Fixed

  • Workflow will exit with "No files match pattern" if no suitable files are found to basecall
    • Ensure to set --dorado_ext to fast5 or pod5 as appropriate

[v0.0.1]

  • Initial release of wf-basecalling supporting the Dorado basecaller

[v0.0.0]

  • Initialised wf-basecalling from wf-template #30ff92d