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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

  Danderson123

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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

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Commits on Jun 29, 2021

• 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 14, 2021

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

  Danderson123

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Commits on Jun 11, 2021

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

  Danderson123

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

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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 May 28, 2021

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

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Commits on May 21, 2021

• Add script to convert GPS csv files to json

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• Create GPS_rename_assemblies.py

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Commits on May 20, 2021

• Add scripts to help index GPS data

  Danderson123

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• Adds some flexibility with snakemake and fixes bug in GPS_biosample_extract

  Danderson123

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Commits on May 19, 2021

• Update GPS_extract_biosamples.py

  Danderson123

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• Create GPS_extract_biosamples.py

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