CHANGELOG.md

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.

[v1.5.0]

Fixed

• Parsing of an insert that is split between the start and end of the assembly and is a reverse complement.
• Swap read count plot axis so Sample aliases are readable.
• Incorrectly running Insert QC and outputting Insert statistics when an insert was not present in the assembly.

Changed

• Updated Medaka to v2.0.0
• The default maximum allowed mismatches in the insert primers has changed from 3 to 2.

[v1.4.0]

Added

• --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.
• --medaka_model_path parameter to provide a custom medaka model. This is intended for users testing experimental Medaka models and will not be needed for general use.

Removed

• The now redundant --basecaller_cfg parameter as its value is now automatically detected from the input data on a per-sample basis.

Changed

• Min and max read length determined per sample based on approx_size
• Emit assembly quality stats as part of final workflow outputs
• Trim length parameter can be set to 0.

[v1.3.1]

Added

• Parameter to control number of mismatches allowed in cutsite analysis

Fixed

• Regression causing incorrect raw read counts shown in "Read stats" section of the report.
• INDELS now called from assembly to reference alignment (-m1 added to bcftools mpileup)

[v1.3.0]

Changed

• Updated Medaka to v1.12.0.
• Updated EZCharts to v0.10.0.

Added

• --full_reference parameter to accept a reference of the full construct. If provided, an additional construct QC section will be output in the report which will include reference coverage and percentage identity per sample.
• Additional per-sample output files if --full_reference is provided:
  • BAM: Reference aligned with the assembly in an indexed BAM.
  • Variant stats: BCF stats report with any variants found between reference and assembly.
  • Variant BCF: BCF file with all variants found between reference and assembly.
  • BAM stats: Stats report from alignment of provided reference with assembly.
• Optional linearisation efficiency section in the report, added when the cut_site column is supplied in the sample sheet.
• Support for full_reference and insert_reference columns in the sample sheet (to provide different references for individual samples). The MSA for insert analysis will group samples based on insert_reference.
• Workflow now additionally accept BAM as input by using the --bam parameter.

Fixed

• Update plannotate version to v1.2.2 which fixes error that occurs when a feature contains a float.

Removed

• The --medaka_model parameter (since the appropriate Medaka model is now automatically determined from the input data). If the input data are lacking information on the model that was used to basecall them, the basecall model must be provided with --basecaller_cfg. Otherwise the workflow will fail.

[v1.2.0]

Added

• Reinstate Canu assembler alongside Flye.
• --assembly_tool parameter with options canu and flye (default: flye).
• --client_fields parameter to add extra info to the report

[v1.1.0]

Changed

• Ensure repetitive regions are marked on the dot plot by reducing the threshold for suppressing repeats inside exact matches.

Added

• --large_construct parameter for assembly of larger constructs including Bacterial Artificial Constructs(50,000-300,000bps).

[v1.0.0]

Removed

• Parameters --min_barcode and --max_barcode
• Default local executor CPU and RAM limits.

Changed

• Parameterised Flye meta option (--non_uniform_coverage) for non-uniform data and defaulted to false.

Fixed

• Now handles sample aliases consisting only of numbers.

[v0.5.3]

Fixed

• Squashed assembly stats section downsampled plots.

Added

• Log a warning when sample sheet approx size column is being used instead of approx size parameter.

[v0.5.2]

Fixed

• Deconcatenate only if the assembly is not of the approx. expected size.
• .gbk output file has the actual sequence for the origin

Added

• Dotplot allowing to visualize the repetitive regions in assemblies.
• If approximate size is <=3000 set Flye min overlap to 1000.

[v0.5.1]

Added

• Additionally output plannotate annotations as a GenBank (.gbk) file.

Removed

• Remove plasmid length column from plannotate feature table.

Changed

• Strand column of plannotate feature to use + and - notation.
• Default --primers parameter is now set to null.

Fixed

• If --host_filter provided the fastcat stats will be included in the report.

[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