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Commits on Jul 24, 2021

• 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

• 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

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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

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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

• 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

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

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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

  Danderson123

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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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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

• 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

• Bug fix in isolate metadata scripts

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Commits on May 28, 2021

• A number of improvements for the scalability of the pipeline.

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Commits on May 21, 2021

• Append GPS metadata to isolate metadata files if indexing GPS isolates. Also ensure isolate labels are GPS lane_ids

  Danderson123

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• Add script to convert GPS csv files to json

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Commits on May 20, 2021

• Adds some flexibility with snakemake and fixes bug in GPS_biosample_extract

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Commits on May 19, 2021

• Update extract_genes.py

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• Fixes bug where previously seen genes were not found and assigned new annotations and improves efficiency of updating the panaroo outputs

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Commits on May 18, 2021

• Import label: biosample pairs for current and previous run and merge together

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• Fix bugs where genes were incorrectly annotated with duplicate consistent names

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Commits on May 17, 2021

• Initial attempt to query isolates against PRG

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Commits on May 14, 2021

• Delete extract_genes copy.py

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• parallelise integration of query isolates, then extract gene information for the query isolate

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Commits on May 13, 2021

• Remove commas from panaroo descriptions

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Commits on May 12, 2021

• Remove duplicate of elastic search client and improve efficiency of update gene_data.csv

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Commits on May 11, 2021

• Merge previous panaroo output into current to prevent loss of data if run terminates prematurely

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• Add back in panaroo frequency and ensure panarooDescription is list instance

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• Fix bug where updated Panaroo name would be missing from panaroo outputs in some cases

  Danderson123

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