piranha v1.3.1

Release notes

• Some minor updates, including handling special case of argument when entry value is 0, making sure it is applied to the configuration. Issue #247
• Recursively search the directory tree for FASTQ files, check if the parent directory is barcodeXX, catalogue barcode dirs found and overwrite input path with the path to barcode dirs if it is not already the same. Issue #186
• Issue #178 resolved, in config table now

piranha v1.3

Release notes

• Merge in updates from wt-dev branch
• Split reference mapping now choose best score hit, rather than filtering out as ambiguous
• whole genome and pan-ev pipelines removed, now just selects different reference panels
• Masking for low-coverage implemented as a post-hoc processing step informed by information from the pileup
• Docker image updated to cope with tensorflow incompatibility issues

piranha v1.2.5

Bump for tensorflow version pin in Docker image, but to 1.10 this time

piranha v1.2.4

Bumped release to try fix Docker build issues (medaka related).

piranha v1.2.3

• Updated tag for piranha main
• Now contains reference group as a tag

piranha v1.2.2

Release notes

• Update config.py for issue #187
• Removing the new references added that conflict with ones already there for pos control

piranha v1.2.1

Release notes

• Update to phylo, patch for no supp datadir provided.
• Flag for parameter name for phylo in Epi2Me updated
• Demo updated to reflect change to phylo

piranha v1.2

Release notes

• Update to how phylo supplementary data are handled.

An optional set of local sequences can be supplied to supplement the phylogenetic analysis. To supply them to piranha, point to the correct directory using -sd,--supplementary-datadir. The sequence files should be in FASTA format, but do not need to be aligned. To allow piranha to assign the sequences to the relevant phylogeny, the sequence files should have the reference group annotated in the header in the format display_name=Sabin1-related, for example.

This supplementary sequence files can be accompanied with csv metadata files (one row per supplementary sequence) and this metadata can be included in the final report and annotated onto the phylogenies (-smcol/--supplementary-metadata-columns). By default, the metadata is matched to the FASTA sequence name with a column titled sequence_name but this header name can be configured by specifying -smid/--supplementary-metadata-id-column.

Piranha will iterate accross the directory supplied and amalgamate the FASTA files, retaining any sequences with display_name=X in the header description, where X can be one of Sabin1-related, Sabin2-related, Sabin3-related or WPV1. It then will read in every csv file it detects in this directory and attempts to match any metadata to the gathered fasta records. These will be added to the relevant phylogenies.

• Update to how local database is updated

If you supply a path to the -sd,--supplementary-datadir for the phylogenetics module, you have the option of updating this data directory with the new consesnsus sequences generated during the piranaha analysis. If you run with the -ud,--update-local-database flag, piranha will write out the new sequences and any accompanying metadata supplied into the directory provided.

The files written out will be in the format runname.today.fasta and runname.today.csv. For example, if your runname supplied is MIN001 and today's date is 2023-11-05, the files written will be:

MIN001.2023-11-05.fasta
MIN001.2023-11-05.csv with the newly generated consensus sequences and accompanying metadata from that run.
Note: if supplying the supplementary directory to piranha on a subsequent run, your updated local database will be included in the phylogenetics. However, piranha will ignore any files with identical runname.today patterns to the active run. So, if your current run would produce files called MIN001.2023-11-05.fasta and MIN001.2023-11-05.csv, if those files already exist in the supplementary data directory, they will be ignored. This is to avoid conflicts if piranha is run multiple times on the same data.

• Piranha now runs on EPI2ME
• Phylo pipeline added to github actions

piranha v1.1.2

Release notes

• Temp output file that describes the treatment of every read (mapped, unmapped, filtered, why it was filtered)
• aln_block_len now configurable (default still 0.6 of the min read length|)
• logos in the report are now clickable to go to the website and to go to repo
• ID'ed a bug in config parsing, newer arguments were being ignored. now updated to use globals() python to find defined in config, rather than an explicit set of arguments that needs maintaining
• Two new lang dict keys for info on piranha and how to cite it in the report (currently biorxiv link)
• show only flagged seqs table in report if there are flagged seqs
• Colour by whether cns could be generated (issue #131)
• rm eng and french specific reports
• Update local database flag added, but need to supply supp seqs
• display name added to local db, but think this should change (legacy from rampart) **
• fixing positive and negative parsing when using config.yaml
• Updating eg report son website to contain phylo and configuration table
• fixing metadata merging bug between barcodes.csv and supplementary_metadata.csv

piranha v1.1.1

Release notes

• Fix for issue #162 which was introduced with update to fasta header format
• Big alteration to fasta header formatting now for issue #159
  Consensus fasta header format now includes a record id and record description set of fields. ID will always be consistent, and empty if certain fields not provided. Description dynamic, and can have extra info included with --all-metadata-to-header flag

>SAMPLE|REFERENCE_GROUP|CNS_ID|EPID|SAMPLE_DATE barcode=barcode01 variant_count=8 variants=17:CT;161:CT;427:GA;497:AC;507:CT;772:AG;822:CT;870:CA reference=Poliovirus3-Sabin_AY184221

Where the ID is: SAMPLE|REFERENCE_GROUP|CNS_ID|EPID|SAMPLE_DATE
And the description is: barcode=barcode01 variant_count=8 variants=17:CT;161:CT;427:GA;497:AC;507:CT;772:AG;822:CT;870:CA reference=Poliovirus3-Sabin_AY184221

• For issue #156 can now colour by call as well in the phylogeny