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Commits on Jul 24, 2021

• Merge branch 'main' into dev

  Danderson123

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• Add function to standardise species names, add try and except block to extract ENA metadata and add script to modify elastic entries

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Commits on Jul 7, 2021

• Merge pull request #18 from bacpop/dev

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• Add function to search through ENA assemblies and WGS runs, gunzip in extract_entrez_information, add function to standardise species names

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Commits on Jul 5, 2021

• Adjust merge runs rule depending on conditions

  Danderson123

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• Add isolate metadata to list of isolates per gene, use wget to retrieve Blackwell assemblies, add options not not index and add script to extract ESC_ metadata

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Commits on Jul 1, 2021

• Add. option to index ESC data and make supplementing isolate metadata more generalisable

  Danderson123

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Commits on Jun 29, 2021

• Fix alignment bug where MAFFT was run on single sequences

  Danderson123

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• Adds list of annotated genes to Blackwell assemblies, adds the option to generate a subsample of alignments based on a list of isolates, indexes a list of isolate metadata for each gene, moves the …

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Commits on Jun 18, 2021

• Merge branch 'main' into dev

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• Add GPS metadata to isolate read metadata if specified, index genes found in isolates in isolate metadata SQL table and supplement gene metadata SQL table with detailed isolate metadata

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Commits on Jun 16, 2021

• Store gene metadata in Azure SQL database

  Danderson123

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Commits on Jun 15, 2021

• Comment out SQLite table creation and remove redis docs

  Danderson123

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• Change indexing of gene metadata from redis to sqlite for server-less integration into the API.

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Commits on Jun 14, 2021

• Merge pull request #17 from bacpop/dev

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• Add docs for locally hosting Redis servers

  Danderson123

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• Store array of isolates containing genes in a redis db instead of as additional fields with elastic.

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• Update README.md

  Danderson123

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• Add script to calculate the rankScore of isolates based on the available metadata and add GPS option back to Snakemake pipeline.

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Commits on Jun 11, 2021

• Save assembled reads to a temp dir and remove after script has finished running

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• Only calculate score for contamination if mash output is present. This will not be present if no reads are available.

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• Add script to calculate a rank score for isolates based on the available metadata

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• Calculate assembly statistics if Blackwell assemblies are available. Also ensure all non-filtered rows of the mash output are added to the metadata JSONs.

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• Only add mash row to isolate metadata if 3 or more matching hashes and the match is not a phage.

  Danderson123

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• Add new rules to run mash and extract species purity. Also adds some helper scripts to retrieve assembled reads and extract population wide assembly statistics.

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Commits on Jun 8, 2021

• Add new snakemake rule to run mash screen on reads and assemblies

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Commits on Jun 7, 2021

• Merge branch 'main' into dev

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• Incorporate script to update document information by index, improve efficiency of update panaroo outputs,

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Commits on Jun 1, 2021

• Only update gene information if cluster id is in gene dataframe

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Commits on May 31, 2021

• Update README.md

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• Bug fix in isolate metadata scripts

  Danderson123

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Commits on May 28, 2021

• Update README.md

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• Update README.md

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• Merge pull request #11 from bacpop/dev

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• Remove references to GPS dataset in snakefile. The unedited version is on the GPS branch.

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