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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.

[v1.0.2]

Fixed

  • Incorrect CPU use specification for the medakaVariant process.

[v1.0.1]

Changed

  • Default for --reads_downsampling_size to 1500 to limit memory usage.
  • Default for --medaka_target_depth_per_strand to 150 as the workflow now supports longer amplicons.

Fixed

  • The workflow failing when a sample had only a single read.

[v1.0.0]

Added

  • Memory requirements for each process.

Changed

  • Reworked docs to follow new layout.

[v0.6.2]

Fixed

  • The de-novo QC stage failing when not a single input read re-aligns against the draft consensus.

[v0.6.1]

Changed

  • More informative warnings for failed samples in the report intro section.

[v0.6.0]

Added

  • Assembly step to de-novo consensus mode to handle longer amplicons. README was updated accordingly.

Removed

  • Default local executor CPU and RAM limits

[v0.5.0]

Changed

  • Names of barcoded directories in the sample sheet now need to be of format barcodeXY.

Added

  • Support for specifying reference sequences for individual samples with an extra "ref" column in the sample sheet.

[v0.4.1]

Changed

  • The workflow now also emits VCF index files as well as BAM / VCF index files for combined outputs when running with --combine_results.

Fixed

  • Emitting an empty consensus FASTA file when consensus generation failed in certain situations. Instead, no file is emitted.
  • Now uses the downsampled BAM for medaka annotate.

Removed

  • Misleading allelic balance statistic in report.

[v0.4.0]

Added

  • Running the workflow without a reference will switch the workflow to "no-reference mode" and will use SPOA to construct a consensus sequence de novo.

[v0.3.5]

Changed

  • The workflow now also outputs BAM index files.

[v0.3.4]

Changed

  • The workflow now downsamples reads for each amplicon to be in the suitable depth range for Medaka.

[v0.3.3]

Added

  • MacOS ARM64 support.

[v0.3.2]

Changed

  • Updated Medaka to 1.9.1.

[v0.3.1]

Changed

  • No longer publishes empty result files (BAM, VCF, consensus FASTA) for samples which do not have any reads left after pre-processing and filtering.
  • Now uses Medaka v1.8.2. Options for basecaller_cfg were updated accordingly. The default now is [email protected].
  • The per-sample summary table in the report no longer shows sample metadata columns unless metadata was provided by the user via a sample sheet.

[v0.3.0]

Changed

  • VCF files now use the sample alias as sample name instead of SAMPLE.
  • The reference FASTA file with sanitized sequence headers (with :, *, and whitespace replaced with _) which is used by the workflow internally due to some tools not tolerating these symbols in the sequence IDs is now also published alongside the other results.

Added

  • Parameter --combine_results to also output merged BAM and VCF files.

[v0.2.3]

Fixed

  • The workflow now prints a warning when there are no reads after filtering / preprocessing and produces a truncated report showing only the pre-processing stats table.

[v0.2.2]

Fixed

  • Bug where the mosdepth process would fail if the length of a reference sequence was smaller than the number of depth windows requested.

[v0.2.1]

Changed

  • GitHub issue templates
  • Example command to use demo data.

[v0.2.0]

Changed

  • Instead of dropping variants with DP < min_coverage, set their FILTER column to LOW_DEPTH in the results VCF.
  • Bumped minimum required Nextflow version to 22.10.8.
  • Enum choices are enumerated in the --help output.
  • Enum choices are enumerated as part of the error message when a user has selected an invalid choice.

Fixed

  • Replaced --threads option in fastqingress.nf with hardcoded values to remove warning about undefined param.threads.

[v0.1.3]

Added

  • Consensus sequences and BAM files as output files.

[v0.1.2]

Added

  • Configuration for running demo data in AWS.
  • Tags for epi2melabs desktop app.

[v0.1.1]

Fixed

  • Reference not being required by the schema.
  • Bug in documentation that prevented blog post from building.

[v0.1.0]

  • First release.