v0.3.1

Changed

• No longer publishes empty result files (BAM, VCF, consensus FASTA) for samples which do not have any reads left after pre-processing and filtering.
• Now uses Medaka v1.8.2. Options for basecaller_cfg were updated accordingly. The default now is [email protected].
• The per-sample summary table in the report no longer shows sample metadata columns unless metadata was provided by the user via a sample sheet.

v0.3.0

Changed

• VCF files now use the sample alias as sample name instead of SAMPLE.
• The reference FASTA file with sanitized sequence headers (with :, *, and whitespace replaced with _) which is used by the workflow internally due to some tools not tolerating these symbols in the sequence IDs is now also published alongside the other results.

Added

• Parameter --combine_results to also output merged BAM and VCF files.

v0.2.3

Fixed

• The workflow now prints a warning when there are no reads after filtering / preprocessing and produces a truncated report showing only the pre-processing stats table.

v0.2.2

Fixed

• Bug where the mosdepth process would fail if the length of a reference sequence was smaller than the number of depth windows requested.

v0.2.1

Changed

• GitHub issue templates
• Example command to use demo data.

v0.2.0

Changed

• Instead of dropping variants with DP < min_coverage, set their FILTER column to LOW_DEPTH in the results VCF.
• Bumped minimum required Nextflow version to 22.10.8.
• 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.

Fixed

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

v0.1.3

Added

• Consensus sequences and BAM files as output files.

v0.1.2

Added

• Configuration for running demo data in AWS.
• Tags for epi2melabs desktop app.

v0.1.1

Fixed

• Reference not being required by the schema.
• Bug in documentation that prevented blog post from building.

v0.1.0

First release.