v1.4.2

Changed

• Reconciled workflow with wf-template v5.5.0.
• Increasing memory retries for flye deNovo process

Fixed

• makeReport process used to fail with unaligned (u)BAMs as input because unaligned bams were excluded by default by xam_ingress. We fixed this by setting xam_ingress to keep the unaligned files as well.
• bam and bai files from mapping the reads to the reference or draft assembly, depending on mode used, were previously missing from the output directory. They are now included.
• Single sample reports incorrectly displaying 'de novo assembly failed' on successful samples.

v1.4.1

Added

• Flye stats output and report

Changed

• Reconciled workflow with wf-template v5.3.0
• Filtering samples with no data on meta.n_seqs instead of presence of fastq file post ingress

v1.4.0

Changed

• Reconciled workflow with wf-template v5.2.5.
• Report wording.
• Updated Medaka to v2.0.0.

v1.3.0

Added

• Workflow now accepts BAM as well as FASTQ files as input (using the --bam or --fastq parameters, respectively)
• --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice.

Removed

• The --basecaller_cfg, --medaka_consensus_model, and --medaka_variant_model parameters as the appropriate Medaka model is now automatically determined from the input data.

Changed

• New docker images for resfinder and mlst.
• Updated Medaka to v1.12.0.
• Updated minimum computer specs as flye was not performing robustly.

v1.2.0

Added

• client_fields parameter to allow input of a JSON file of key value pairs to display on output reports.
• min_read_length parameter to remove reads below specified length (default 1000bp) from downstream analysis, to improve de novo assembly process
• Salmonella serotyping with SeqSero2

Fixed

• Duplicate entries in Pointfinder processing

v1.1.1

Fixed

• Report generation when Resfinder fails

v1.0.0

Added

• Cloud support for the workflow within the EPI2ME Application.

Changed

• Documentation

v0.4.0

Added

• MacOS ARM64 support
• New parameter --flye_opts for passing additional arguments to flye.

Changed

• Clarify docker is default in README

Fixed

• De novo assembly failing due to low coverage in some situations.

v0.3.3

Fixed

• Overwrites in Nextflow config implemented incorrectly

Changed

• Updated Medaka to 1.9.1.

v0.3.2

Fixed

• Edge case where medaka variant output is unsorted and causes medaka annotate to exit

Changed

• Bumped minimum required Nextflow version to 23.04.2.
• Now uses Medaka v1.8.2 with updated models.
• Options for the --basecaller_cfg parameter were updated. The default is now [email protected].