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2.0.0 Release #18

Merged
merged 85 commits into from
Apr 19, 2024
Merged

2.0.0 Release #18

merged 85 commits into from
Apr 19, 2024

Commits on Mar 12, 2024

  1. Updating nf-core .github/workflows and .pre-commit-config.yaml files

    @kylacochrane
    kylacochrane committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. Fixing errors associated with nf-core lint

    @kylacochrane
    kylacochrane committed Mar 13, 2024
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  2. Adjusted test.config max_memory

    @kylacochrane
    kylacochrane committed Mar 13, 2024
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  3. Updated branch.yml to reference phac-nml

    @kylacochrane
    kylacochrane committed Mar 13, 2024
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  4. Merge pull request #4 from phac-nml/nf-core-linting 

    Updating files associated with nf-core linting issues
    @kylacochrane
    kylacochrane authored Mar 13, 2024
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Commits on Mar 14, 2024

  1. Committing local changes before rebasing origin/dev

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  2. Fixed file formatting and linting

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  3. Adding the KRACKEN mini_gut database

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  4. Changed db PATH to kraken branch to access minigut_kraken db

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  5. Updates for functionality of pipeline

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  6. fixed EC whitespace in kraken2/main.nf

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  7. Added when statement to kraken module

    @kylacochrane
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  8. Set workflow variable meta.single_end and updated kraken module

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  9. Separated kraken module inputs so workflow can have separate channels

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  10. Separated output entries

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  11. Updated workflow kraken_db channel

    @kylacochrane
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  12. Updated nextflow_schema.json

    @kylacochrane
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  13. Updated kraken module to compress output txt and tsv files

    @kylacochrane
    kylacochrane committed Mar 14, 2024
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  14. Formatting changes

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Commits on Mar 15, 2024

  1. Merge pull request #5 from phac-nml/kraken 

    Kraken Module Addition
    @kylacochrane
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  2. Removed IridaNextExample modules/tests/data and inclusion in workflow

    @kylacochrane
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  3. Merge pull request #6 from phac-nml/remove_irida_modules 

    Removed IridaNextExample modules/tests/data
    @kylacochrane
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Commits on Mar 21, 2024

  1. Adding BRACKEN module and functionality (#7) 

    * Adding the BRACKEN modules; updating modules/workflow to match; added python script for bracken

* Formatting and troubleshooting

* Update workflow; input taxonomic_level as Channel.value; remove .collect()

* Removed print statements for debugging

* Removed print statements for debugging

* Fixed formatting with EC

* Removed adjust_bracken.py file: meant for a different module

* Updated files for GitHub testing of pipeline

* Added mini kraken/bracken database for testing

* Cleaned kmer_dist file in minidb

* Added comment to bracken/main.nf
    @kylacochrane
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  2. Adding the ADJUST_BRACKEN module and python script

    @kylacochrane
    kylacochrane committed Mar 21, 2024
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  3. Update README.md

    @kylacochrane
    kylacochrane authored Mar 21, 2024
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  4. Update README.md

    @kylacochrane
    kylacochrane committed Mar 21, 2024
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  5. Update README.md

    @kylacochrane
    kylacochrane authored Mar 21, 2024
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  6. Updated python script comments

    @kylacochrane
    kylacochrane committed Mar 21, 2024
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  7. Merge pull request #8 from phac-nml/adjustbracken 

    Adding the ADJUST_BRACKEN module and python code
    @kylacochrane
    kylacochrane authored Mar 21, 2024
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  8. Added KRONA functionality

    @kylacochrane
    kylacochrane committed Mar 21, 2024
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  9. Merge pull request #9 from phac-nml/krona 

    Added KRONA functionality
    @kylacochrane
    kylacochrane authored Mar 21, 2024
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  10. Added IRIDANextPlugIn

    @kylacochrane
    kylacochrane committed Mar 21, 2024
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  11. Merge pull request #10 from phac-nml/iridanext_plugin 

    Added IRIDANextPlugIn
    @kylacochrane
    kylacochrane authored Mar 21, 2024
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Commits on Mar 25, 2024

  1. Added CI tests for main workflow; Updated corresponding config files

    @kylacochrane
    kylacochrane committed Mar 25, 2024
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  2. Added CI tests to GitHub Actions: ci.yml

    @kylacochrane
    kylacochrane committed Mar 25, 2024
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  3. Separated test database to expand testing options

    @kylacochrane
    kylacochrane committed Mar 25, 2024
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Commits on Mar 26, 2024

  1. Grammar and regrex edits

    @kylacochrane
    kylacochrane committed Mar 26, 2024
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  2. Update README.md

    @kylacochrane
    kylacochrane committed Mar 26, 2024
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  3. Update README.md

    @kylacochrane
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  4. Update test to assess the nextflow_pipeline; make related changes to … 

    …simplify nf-test.config
    @kylacochrane
    kylacochrane committed Mar 26, 2024
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  5. Updated main.nf.test to improve IRIDA Next JSON data structure

    @kylacochrane
    kylacochrane committed Mar 26, 2024
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Commits on Mar 27, 2024

  1. Updated nextflow.config to uncompress IRIDANext JSON

    @kylacochrane
    kylacochrane committed Mar 27, 2024
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  2. Fixed EC errors

    @kylacochrane
    kylacochrane committed Mar 27, 2024
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Commits on Apr 2, 2024

  1. Updated workflow and tests for Azure functionality

    @kylacochrane
    kylacochrane committed Apr 2, 2024
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Commits on Apr 3, 2024

  1. Update README.md

    @kylacochrane
    kylacochrane committed Apr 3, 2024
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  2. Merge pull request #11 from phac-nml/CITests 

    Added CI tests for SpeciesAbundance workflow pipeline
    @kylacochrane
    kylacochrane authored Apr 3, 2024
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  3. Add top5 module for species identification and workflow functionality

    @kylacochrane
    kylacochrane committed Apr 3, 2024
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Commits on Apr 8, 2024

  1. Added module and MERGE_CSV process for IRIDANext JSON formatting

    @kylacochrane
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  2. Updated the iridanext.config file to include TOP_5 results as metadat… 

    …a to JSON file
    @kylacochrane
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  3. Added assert statements to main.nf.test to ensure test data metadata … 

    …is as expected in IRIDANext JSON file
    @kylacochrane
    kylacochrane committed Apr 8, 2024
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  4. EC error fix

    @kylacochrane
    kylacochrane committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. Changed the TOP_5 process to TOP_N, where N is a passed paramter that… 

    … defines the number of top results to keep
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  2. Changed parameter top_results to top_n

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Commits on Apr 10, 2024

  1. Updating bracken_top_n_linelist.py to encode all missing values to: None

    @kylacochrane
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  2. Added assert statements to expand tests

    @kylacochrane
    kylacochrane committed Apr 10, 2024
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  3. Added nf-core CSVTK/CONCAT module and updated workflow to accomodate

    @kylacochrane
    kylacochrane committed Apr 10, 2024
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  4. Removed old MERGE_CSV local/module

    @kylacochrane
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  5. Updated iridanext.config to accomodate module changes for metadata

    @kylacochrane
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  6. Fixed error in workflow/speciesabundance.nf

    @kylacochrane
    kylacochrane committed Apr 10, 2024
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  7. Updated nextflow_schema.json, modules.json, and modules.config files

    @kylacochrane
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  8. Fixed error with nextflow_schema.json file

    @kylacochrane
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  9. Updated function in bracken_top_n_linelist.py

    @kylacochrane
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  10. Added comments to bracken_top_n_linelist.py

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Commits on Apr 11, 2024

  1. Merge pull request #12 from phac-nml/top5 

    Adding modules to pull the top_5 species kraken/bracken results and add the data in the correct format to the IRIDANext JSON file.
    @kylacochrane
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  2. Updated module output nomenclature

    @kylacochrane
    kylacochrane committed Apr 11, 2024
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  3. Update iridanext.config and main.nf.test

    @kylacochrane
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  4. Updated module naming for consistency (kraken2krona)

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Commits on Apr 12, 2024

  1. Added kmer_len as a parameter to set the kmer distribution files used… 

    … by BRACKEN to estimate the abundance at a single taxonomic level
    @kylacochrane
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  2. Added additional workflow parameter to allow Kraken/Bracken database … 

    …files to come from a single shared directory. Updated nextflow.config, nextflow_schema.json, test.config, and main.nf.test to accomodate these changes
    @kylacochrane
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  3. Formatting changes

    @kylacochrane
    kylacochrane committed Apr 12, 2024
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Commits on Apr 15, 2024

  1. Updated README.md

    @kylacochrane
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  2. Changed parameter name from 'combined_db' to 'database' for clarity

    @kylacochrane
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  3. Updated output and usage documentation

    @kylacochrane
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  4. Updated main.nf.test database parameter

    @kylacochrane
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Commits on Apr 16, 2024

  1. Update pyhton script in ADJUST_BRACKEN to output the Adjusted-Kraken-… 

    …Style-Report
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  2. Updated workflow [bracken2krona] to use Adjusted-Kraken-Style-Report … 

    …from ADJUST_BRACKEN and updated module requirements
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  3. Updated documentation

    @kylacochrane
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  4. Fixed main.nf.test

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Commits on Apr 17, 2024

  1. Added additional output tests

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  2. Update the adjust bracken abundances step to report proportions inste… 

    …ad of percentages
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  3. Merge pull request #13 from phac-nml/add_docs 

    Add additional functionality and final documentation for pipeline usage.
    @kylacochrane
    kylacochrane authored Apr 17, 2024
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  4. Updated versioning in CHANGELOG.md and nextflow.config

    @kylacochrane
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  5. Added link to Galaxy-based pipeline for reference

    @kylacochrane
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  6. Merge pull request #17 from phac-nml/version 

    Updated versioning in CHANGELOG.md and nextflow.config
    @kylacochrane
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Commits on Apr 19, 2024

  1. Updated kraken2 process to high

    @kylacochrane
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