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.

v4.1.0

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.

v0.0.5

Added

• Software versioning report example.

v0.0.4

Changed

• Version bump to test CI