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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.

[v0.5.0]

Changed

  • The report has been updated and re-ordered to improve usability.
  • Default basecaller cfg is now dna_r10.4.1_e8.2_400bps_sup@v4.2.0.
  • Docker will use an ARM platform image on appropriate devices.

Fixed

  • Updated basecaller cfg model options.
  • Workflow will still output report if there are no assemblies.

[v0.4.0]

Added

  • Documentation updated to include workflow steps.
  • Full plasmid assembly mean quality table in report.
  • Output a fastq of the final assembly.
  • Insert reference, if provided, will now be used to variant call insert consensus with bcftools.

Removed

  • Unused packages from the container.

Changed

  • 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
  • Bumped minimum required Nextflow version to 22.10.8
  • Updated GitHub issue templates to force capture of more information.
  • Reference parameter changed to --insert_reference.
  • Updated example command displayed when running --help
  • Parameter--approx_size_sheet no longer accepted, instead use sample sheet with optional additional column approx_size.
  • Any sample aliases that contain spaces will be replaced with underscores.

Fixed

  • Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads
  • Annotation output bed file has correct notation for strand.

[v0.3.1]

Added

  • Configuration for running demo data in AWS

[v0.3.0]

Added

  • Flye replaces canu as the assembler tool.

[v0.2.13]

Changed

  • Updated to Oxford Nanopore Technologies PLC. Public License.

Fixed

  • Amended raw QC stats to show data before filtering by assembly_size parameter.

[v0.2.12]

Fixed

  • Bug where the workflow wouldn't run properly when --approx_size_sheet was used.

Changed

  • Now uses new fastq_ingress implementation.

[v0.2.11]

Fixed

  • Provide medaka model for each assembly to fix bug.

[v0.2.10]

Fixed

  • Replace spaces with tabs in medaka model TSV to fix bug.

[v0.2.9]

Fixed

  • Medaka models added to container

[v0.2.8]

Changed

  • --basecall_cfg is now used to determine suitable Medaka model, alternatively provide the name of a model with --medaka_model to override automatic selection.

[v0.2.7]

Changed

  • Updated description in manifest

[v0.2.6]

Removed

  • -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead

Added

  • nextflow run epi2me-labs/wf-clone-validation --version will now print the workflow version number and exit

[v0.2.5]

Fixed

  • Filter host step not outputting approx_size.

Updated

  • Use groovy script to ping after workflow has run.

[v0.2.4]

Added

  • Error handling for no annotations found for an assembly.
  • Windows parameter so Canu can run on windows

Fixed

  • Plannotate dictionary keys can contain any characters.
  • Sanitize fastq intermittent null object error.

[v0.2.3]

Changed

  • Change params.threads to task.cpus

[v0.2.2]

Changed

  • Fastqingress metadata map.
  • Sample status now collected from tuples.

[v0.2.1]

Changed

  • Plannotate read/write database requirement fix
  • approx_size_sheet param instead of sample_sheet
  • Set out_dir option type to ensure output is written to correct directory on Windows

[v0.2.0]

Changed

  • Better help text on CLI.
  • Fix issue with S3 file inputs.

Updated

  • Plannotate to version v1.2.0

[v0.1.9]

Added

  • Param for fast option in Canu assembly

[v0.1.8]

Changed

  • New docs format

[v0.1.7]

Fixed

  • Sample sheet encoding
  • Min max barcodes integer types

Changed

  • Moved bioinformatics from report to seperate processes

Added

  • Ability to define approx_size of sequence per sample in sample_sheet
  • Insert length to table
  • Output annotation bed files per sample

[v0.1.6]

Changed

  • Update schema for epi2melabs compatibility

Fixed

  • Make use of the canu_useGrid parameter

[v0.1.5]

Added

  • Singularity profile to config.
  • Ping telemetry file.
  • Handle more fastq input directory structures.

Fixed

  • db_directory description and explained in README
  • db_directory param updated to match s3 folder name

Changed

  • Use downsampled samples for polish assembly step.

[v0.1.4]

Added

  • Option to add suffix to HTML report name.
  • Error message if fastq input file evaluates to null.

[v0.1.3]

Fixed

  • Default Primers parameter txt to tsv.

[v0.1.2]

Added

  • Fastcat stats plots in tabs for pass and failed samples.
  • Version and parameter tables.
  • Per barcode number of reads.
  • Insert sequences output.
  • MSA of inserted sequences.

Fixed

  • Order samples lexicographically.

Changed

  • Use Canu for assembly instead of Flye.
  • Trim input sequences.

[v0.1.1]

Fixed

  • Corrected number of input channels for host_reference process.
  • Remove duplicate output files.
  • Help message parameters reflect config.

[v0.1.0]

Added

  • Plannotate for plasmid annotation and visualization.
  • Per sample pass or fail error message in CSV.
  • Plasmid annotation feature table output CSV.

Changed

  • Updated project to use latest practices from wf-template.

Fixed

  • Incorrect specification of conda environment file in Nextflow config.

[v0.0.4]

Added

  • Fix report naming to be consistent with other projects

[v0.0.3]

Added

  • Optional --prefix flag for naming outputs

[v0.0.2]

Added

  • --no-reconcile flag for a simpler and quicker overall pipeline

Changed

  • simplified assembly outputs, to only emit the final polished assembly

[v0.0.1]

  • First release