1.2.4

What's Changed

• Update vcftagprimersites.py by @mattloose in #123

New Contributors

• @mattloose made their first contribution in #123

Full Changelog: v1.2.3...v1.2.4

1.2.3

Minor update to fix a dependency bug resulting in two forks of pyvcf being installed alongside another (the cause of [#119]) as well as an update to the medaka version pinning for access to more models, and longshot 0.4.5 to fix [#117] as suggested in the same issue.

Full Changelog: 1.2.2...v1.2.3

1.2.2

Re-implemented the artic-tools scheme downloader in python to avoid a bug introduced with V4.1 of the artic primers (4.1 is a float not an integer).

1.2.1

Patched a bug in the previous release where --strict was failing due to un-indexed VCF being provided to artic-tools.

Also:

• removes the reliance on a MultiQC artic module, instead we generate some stats from the align_trim output and the vcf_check output, storing these as a JSON file which MultiQC can munch on. I've included this as a feature enabled by --strict, so the extra files aren't produced using the existing pipeline. This also fixes an issue some users were encountering with pip dependencies for not being installed correctly
• updates the doc with some missing minion sub commands

1.2.0

Brief overview of updates:

• Updates environment to bump medaka to v1.0.3 and adds artic-tools
• Adds a --no-longshot flag to minion, which prevents longshot running in the medaka workflow and instead uses medaka annotate to add info to the VCF.
• Adds a prefilter before filtering the medaka VCFs to bin vars with <2 read in support and var quality < 20, instead of writing them to the FAIL VCF and contributing to the consensus mask
• Because of the prefilter, the longshot and medaka filters in vcf_filter have been combined to a single filter as they perform the same function.
• Adds --strict flag to minion to enable both primer scheme checking (for ARTIC format conventions) and filtering of the merged VCF to remove variants that are present only once in amplicon overlap regions, or are present in primer binding sites.
• Adds --scheme-version flag to minion to give user option of specifying primer scheme version. Scheme version can be omitted and the original behaviour (schemename/V1) is still used preferentially over the new flag. Default will remain 1 but the latest available scheme can be specified using 0. If the scheme name is not found using the original logic (combining scheme name, scheme dir and scheme version), minion will attempt to download the scheme from the ARTIC repos (only nipah, ebola, scov2 available atm). The minion command can now be simplified a bit by dropping --scheme-directory and autodownload schemes, e.g.:
  artic minion --medaka --read-file test-data/*.fast[aq] scov2/V3 MT007544
• Rearranges the variant calling code block in minion, removing the need to split the BAMs by readgroup as medaka performs BAM filtering in place - resulting in fewer bam copies.
• Adds some code comments throughout minion to document pipeline steps.
• Moves some file opening closer to where they are being used.
• Cleans repo to remove an old fast5 which was lurking in the commit history and causing slow repo downloads. This improves the fix from #38. It should be noted that anyone wanting to make a PR will need a fresh pull/fork of the repo from today.
• Adds multiqc (artic fork) to the conda environment (via pip), which produces amplicon coverage plots and variant quality information. This closes #51 as now amplicon coverage is computed from the align_trim report. Plots are now optionally produced by the user after the pipeline is run and can be collated across runs.
• Deprecates plot_amplicon_depth script and removed associated dependencies. This has been a headache for pipeline users on HPC schedulers etc. Multiqc now replaces this functionality and the plotting is more accurate and optional.
• Requires --medaka-model to be provided if --medaka is set during artic minion runs.
• Updates docs.

Notes:

• The new --no-longshot flag causes more Ns in the consensus as we do not achieve the same filtering as longshot was doing, ending up with a few more vars appearing in our VCF fail file, which are applied to the mask.
• A bug in medaka means that when medaka annotate is used instead of longshot (via the new flag), INDELs will be silently dropped as medaka incorrectly reports no read support.

1.1.3

Patch update to fix a primer merging bug.

As pointed out by Shirlee Wohl - the merge_sites function was producing the intersection, not union, between alts and canonicals for right primers.

1.1.2

Patch release:

• fixes the primer parsing for schemes with no non-alt partners (thanks @m-bull)
• adds a pre-histogram binning sort to the plotting script, which should stop the monotonic sort error that crops up for unsorted primer schemes
• fixes a tqdm import error seen by conda during the pytests

1.1.1

This release pulls in the previous two release candidates and adds a few minor patches:

• masking now uses pool depths
• test data is now downloaded during tests rather than shipped with the repo
• minion pipeline now includes amplicon depth plots
• dependency version bumps

v1.1.0-rc2

• Update medaka to 0.12.1
• Update nanopolish to 0.13.0
• Add --no-indels flag
• Fix Longshot dumping out variants due to strand bias filter in Medaka pipeline

1.1.0-rc

v1.1.0-rc1:

Support for read groups:
Support ‘pool’ read groups taken from BED file, e.g.:

• nCoV2019_1
• nCoV2019_2
  These can be helpfully viewed in the Tablet viewer.
  Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination

Update to nanopolish 0.12.5 fo more informative VCF output
Change nanopore filtering to support new VCF output (e.g. strand-bias)

Support indels with bcftools consensus
Longshot added to Medaka to permit filter VCF on depth

New workflow model - all commands run "one per sample", script nanopolish index

Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather'

Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail

Support for amplicons v3 format file (Will Rowe)

Test suite (Will Rowe)

Documentation (Will Rowe)

Remove old deprecated code (Will Rowe)