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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.

[v5.3.1]

Changed

  • Datamodel-codegen now uses subclasses in Enum classes.

[v5.3.0]

Fixed

  • Collections of sorted XAM files eligible for merge will no longer be needlessly re-sorted before merge.

Added

  • reheader_samstream script to be used to restore a XAM header when aligning a XAM with the samtools bam2fq->minimap2 idiom.

Changed

  • Supported multiple variation files for a single XAM file in configure_igv.

[v5.2.6]

Changed

  • Updated wf-common to shad28e55140f75a68f59bbecc74e880aeab16ab158 improving legends and hovers for ezCharts plots (v0.11.2).

[v5.2.5]

Changed

  • Updated wf-common to shae58638742cf84dbeeec683ba24bcdee67f64b986 fixing SeqSummary and SeqCompare plots in ezCharts (v0.11.0).

[v5.2.4]

Added

  • meta keys src_xam and src_xai pointing to the input XAM/XAI files.
  • src_xam and src_xai will be set to null if multiple XAM per sample are provided, if files are hosted in S3 or if the files are altered by ingress.nf.

Changed

  • Updated wf-common to sha4a766a8333dbb72086b117c6eefba08e8ef7d76e to improve report layouts in EPI2ME Desktop with ezCharts (v0.10.2).
  • Compare only SQ SN,LN,M5 when determining if collection of XAM headers have been aligned to conflicting references.
  • Automatically emit the igv.json file upon generation.

Fixed

  • Resumed workflow leading to mismatched (BAM, BAI) validateIndex pairs when calling xam_ingress more than once.
  • Broken Markdown rendering of install and run section of README in desktop application.

[v5.2.3]

Changed

  • Updated wf-common image to shad399cf22079b5b153920ac39ee40095a677933f1 to include latest fastcat (v0.18.6).

[v5.2.2]

Changed

  • Matching RG.IDs found in XAM headers are now combined across all input XAM for a particular sample and emitted once, instead of emitting new RG.IDs for each XAM file.
  • Bumped wf-common to shab540ba556d0d8c38bea8fec520f0bdedd9e59520.

Fixed

  • Non-determinstic catting and merging of XAM files during ingress.

[v5.2.1]

Changed

  • Updated epi2melabs to v0.0.56 to allow schemas without a demo_url field.

[v5.2.0]

Added

  • Support for CRAM alignment format when creating IGV config files.
  • Support for an optional "analysis_groups" column in the sample sheet providing grouping information for the input samples.

Changed

  • Basecall models are now obtained from FASTQ / BAM input files via fastcat / bamstats output and added to sample meta map.

[v5.1.4]

Added

  • Support for creating IGV JSON config files.

Changed

  • Updated ezcharts to v0.9.1, showing coverage and accuracy plots when available.

[v5.1.3]

Changed

  • workflow-glue CLI bootstrapping amended to skip imports of all components when not required.

[v5.1.2]

Added

  • xam_ingress reads basecall_model and runid to metamap from RG DS tags.

[v5.1.1]

Fixed

  • xam_ingress failing on BAM files that are lacking a @HD line in the header.

[v5.1.0]

Added

  • Functionality to allow chunking of fastq outputs from ingress. Additional keys in meta information are added to reflect this.

Changed

  • Use 4 threads for bgzip compressions during fastcat process.
  • Updated fastcat to v0.17.0 for faster decompression and on-the-fly run ID summary.
  • Updated to use ezCharts v0.8.0 for report generation.
  • Remove per-read stats from fastcat output by default.

Fixed

  • Ingress code would return stats even when not requested.

[v5.0.4]

Fixed

  • xam_ingress failing to stage S3 BAM indexes.

[v5.0.3]

Changed

  • Bumped wf-common to sha645176f98b8780851f9c476a064d44c2ae76ddf6.

Fixed

  • Refusing to parse valid sample sheet CSV files in certain cases.

[v5.0.2]

Changed

  • Bumped wf-common to sha362c808b4f22ce66f940bef192a1316aec5f4c75.

[v5.0.1]

Added

  • container directive for processes with wftemplate label.
  • Missing label directives for samtools_index process.

Changed

  • Bumped wf-common to shaa0c37a1cad3357e2b5c6fa8b9ebc25ee9ee88879.

[v5.0.0]

Added

  • Argument return_fastq to xam_ingress() to convert the input BAM data to FASTQ format.
  • User provided sample sheet is now published in the output directory as sample_sheet.csv.
  • A check to make sure the sample sheet is a CSV file (and not e.g. .xlsx).
  • n_seqs field to the meta map for fastq_ingress(), containing the number of processed reads of the respective sample.
  • n_primary and n_unmapped for xam_ingress(), containing the number of primary alignments and unmapped reads for the respective sample.
  • Support for indexing of input BAM files within xam_ingress().

Changed

  • Update bug template to new workflow execution possibilities.
  • --client_fields parameter to allow input of a JSON file of key value pairs to display on output reports.
  • Pre-indexed, single BAM files are not sorted within xam_ingress().

[v4.3.0]

Changed

  • Bumped minimum required Nextflow version to 23.04.2.
  • Renamed lib/fastqingress.nf to lib/ingress.nf to reflect its expanded functionality.
  • The documentation has been updated.

Added

  • xam_ingress function for processing (u)BAM data.
  • Git issue bug form requires user to report if the demo data was successful.

Removed

  • Default local executor CPU and RAM limits.

[v4.2.0]

Added

  • 'CWUtil.mutateParam(params, k, v)' can be used to mutate the contents of the global Nextflow parameter map

Changed

  • Workflow uses wf-common container by default
  • Sample meta contains run_ids key which lists all Run IDs observed by fastcat
  • fastqingress processes additionally labelled with fastq_ingress
  • Use literal names to stage process inputs wherever possible and wrap filenames in quotes otherwise.
  • Any sample aliases that contain spaces will be replaced with underscores.

Removed

  • wf-template container is no longer used
  • params.process_label is no longer required

[v4.1.0]

Added

  • Optional required_sample_types field added to fastqingress. The sample sheet must contain at least one of each sample type provided to be deemed valid.
  • Configuration for running demo data in AWS

Changed

  • Updated GitHub issue templates to force capture of more information.
  • Removed glibc hack from post-test script
  • Updated LICENSE to BSD-4-Clause
  • 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

Fixed

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

[v4.0.0]

Added

  • GitHub issues template.
  • Return of metadata with fastqingress.
  • Check of number of samples and barcoded directories.
  • Example of how to use the metadata from fastqingress.
  • Implemented --version
  • fastcat_extra_args option to fastq_ingress to pass arbitrary arguments to fastcat (defaults to empty string).
  • fastcat_stats option to fastq_ingress to force generation of fastcat stats even when the input is only a single file (default is false).

Changed

  • Use bgzip for compression instead of pigz.
  • pre-commit now uses flake8 v5.0.4.
  • Report is now created with ezCharts.
  • The workflow now also publishes the metadata emitted by fastq_ingress in $params.out_dir.
  • fastq_ingress now returns [metamap, path-to-fastcat-seqs | null, path-to-fastcat-stats | null].
  • Bumped base container to v0.2.0.
  • Use groovy script to ping after workflow has run.
  • Removed sanitize fastq option.
  • fastq_ingress now removes unclassified read folders by default.
  • Workflow name and version is now more prominently displayed on start

Fixed

  • Output argument in Fastqingress homogenised.
  • Sanitize fastq intermittent null object error.
  • Add *.pyc and *.pyo ignores to wf-template .gitignore

Note

  • Bumped version to v4 to align versioning with Launcher v4

[v0.2.0]

Added

  • default process label parameter
  • Added params.wf.example_cmd list to populate --help

Changed

  • Update WorkflowMain.groovy to provide better --help

[v0.1.0]

Changed

  • sample_name to sample_id throughout to mathc MinKNOW samplesheet.

Added

  • Singularity profile include in base config.
  • Numerous other changes that have been lost to the mists of time.

[v0.0.7]

Added

  • Fastqingress module for common handling of (possibly multiplexed) inputs.
  • Optimized container size through removal of various conda cruft.

Changed

  • Use mamba by default for building conda environments.
  • Cut down README to items specific to workflow.

Fixed

  • Incorrect specification of conda environment file in Nextflow config.

[v0.0.6]

Changed

  • Explicitely install into base conda env

[v0.0.5]

Added

  • Software versioning report example.

[v0.0.4]

Changed

  • Version bump to test CI.

[v0.0.3]

Changed

  • Moved all CI to templates.
  • Use canned aplanat report components.

[v0.0.2]

Added

  • CI release checks.
  • Create pre-releases in CI from dev branch.

[v0.0.1]

  • First release.