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Version 0.1.0 Release #18

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kylacochrane merged 139 commits intomainphac-nml/gasnomenclature:mainfrom devphac-nml/gasnomenclature:devCopy head branch name to clipboardJun 28, 2024

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Commits on Apr 2, 2024

• updated tracked test data

  

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• Merge pull request #3 from phac-nml/workflow

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• Created initial workflow

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• added initial unit tests

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• removed module tests

  

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• updated expected clusters path

  

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• updated test configs

  

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Commits on Apr 3, 2024

• updated nftest.config

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• updated test outpu path

  

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• updated test output paths

  

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• fixed test data line endings

  

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• updated paths to expected input files

  

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• updated test conf file input paths

  

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• updated params in test configs

  

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• updated schema, and test file line endings

  

  Matthew Wells

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• updated schema types

  

  Matthew Wells

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• Ran prettier

  

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• updated function data types

  

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Commits on Apr 4, 2024

• Merge pull request #4 from phac-nml/workflow

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Commits on Apr 5, 2024

• Update gas_nomenclature.nf

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• Merge pull request #5 from phac-nml/fix-prepFilePaths

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Commits on May 6, 2024

• Updated samplesheet to include 'address' column

  kylacochrane

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• Updated locidex_merge_ref to include all samples, including new query samples

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• Updated expected test results to accomdate all samples in reference

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• EC error fix

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• New module to filter out the new query addresses

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Commits on May 7, 2024

• Added nf-iridanext plugin

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• EC error fix

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Commits on May 8, 2024

• Adding a basic solution for identifying when sample ID's do not match to mlst.json keys

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Commits on May 15, 2024

• Update query filtering process name and add versions

  kylacochrane

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• Updated linting to resolve issues

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• Fixed another linting issue

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• Fixing linting issues, for real this time

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• Merge branch 'filter-new-addresses' into input_check

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• Add new modules/processes: INPUT_CHECK, SAMPLE_FILTER, ERROR_REPORT

  kylacochrane

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• Add corresposonding python scripts; remove unused scripts

  kylacochrane

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• Update iridanext.config to include error_reports

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• Updated workflow

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Commits on May 16, 2024

• Uploading files for new integration tests

  kylacochrane

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• Added new test and configuration files; fixed EC issues

  kylacochrane

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• Improvements to the FILTER_QUERY module

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• EC fix

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• Merge branch 'filter-new-addresses' into input_check

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• Fixed discrepancy with previous merged from filter-new-addresses into filter_query

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• Remove left-overs from pipeline template

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• Fixed linting issue with modules.config

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• Merge INPUT_CHECK and ERROR_REPORT into one module

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• Fixed input_check.py

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• Update iridanext.config

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Commits on May 17, 2024

• Updated workflow to filter sample inputs and removed corresponding module/process

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• Merge branch 'input_check' into add_tests

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• Update main.nf.test to align with changes from input-check branch

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• Updated main.nf.test

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Commits on May 21, 2024

• Merge pull request #10 from phac-nml/add_tests

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  kylacochrane

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• Reverted changes to nf-core module

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• Improvement to workflow

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• Updated workflow

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Commits on May 22, 2024

• Merge pull request #9 from phac-nml/input_check

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• Merge pull request #8 from phac-nml/filter-new-addresses

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• Merge pull request #7 from phac-nml/references-all

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• Merge pull request #6 from phac-nml/samplesheet-update

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• Update URLs in test samplesheets

  kylacochrane

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Commits on May 27, 2024

• Add a module to partition reference sample addresses into hierarchical levels for the gas-call process

  kylacochrane

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• Update workflow to generated expected_clusters file

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• Update test.config

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• Update gas-call expected_results.txt following modification of sample 3 address in expected_clusters file

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• Fixed typo

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• Update parameters for profile_dists and gas_call; Add/update descriptions of various parameters for clarity

  kylacochrane

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• Remove pd_force from nextflow.config

  kylacochrane

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• Removed pd_force argument from profile_dists/main.nf

  kylacochrane

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• update documentation

  kylacochrane

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• Update gm_delimiter parameter

  kylacochrane

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• Fixed defaults for gm_delimiter

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• Fix whitespace

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Commits on May 28, 2024

• Update CLUSTER_FILE to split on gm_delimiter

  kylacochrane

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Commits on May 29, 2024

• Raise exception if sample levels are different

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Commits on May 30, 2024

• Updated cluster_file process to use 'error' instead of 'throw Exception'

  kylacochrane

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• Added a cluster_file process test to evaluate samples with different levels

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Commits on Jun 4, 2024

• Add clustering method

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• Comment removed from gas-call main.nf

  kylacochrane

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Commits on Jun 6, 2024

• Removed padding in cluster_file process

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• nextflow.config comment clean up

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• Revise 'input_check' to 'input_assure'; enforce JSON key alteration to match the sample ID if a mismatch is detected

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Commits on Jun 7, 2024

• Remove id_match from meta

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• Fix linting

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• Updated error_message from input_assure

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• fix: correctly escape delimiter in CLUSTER_FILE process

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• Add check to main.nf.test to assert query profile is merged

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• Added success case to cluster_file process test

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• Update README and USAGE documents

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• Remove the --pd_outfmt paramater

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Commits on Jun 10, 2024

• Update python script name to match process: input_assure.py

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• Add 'fair = true' to input_assure process in modules.config for reproducibility

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• Update input_assure.py to include additional check for multiple keys

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• Fixed linting issues

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• Merge pull request #11 from phac-nml/expected-clusters

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Commits on Jun 11, 2024

• Resolved conflicts between dev and update-parameters

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• Merge pull request #12 from phac-nml/update-parameters

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• Update filter_query to accomodate multiple queries

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• Add test for multiple_queries and supporting files

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• Implement 'fair true' in input_check to insure consistent ordering of samples

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• Update file path in samplesheet

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• Added missing expected test file

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Commits on Jun 12, 2024

• Changed cluster_file output filename for clarity

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• Merge pull request #14 from phac-nml/update-filter_query

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• Merge 'dev' into 'input_assure

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• Resolve conflicts between dev and input_assure

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• Add test with gzipped MLST JSON file

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• Added test for mismatched IDs

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• Update paths in samplesheet

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• Fix EC issues

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• Fix EC issues

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• Removed unexpected character (#) in main.nf.test

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Commits on Jun 13, 2024

• Add test data for multiple keyed JSON file

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• Tests added to handle when there are multiple sample entries (keys) in provided MLST JSON file(s)

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• Updated input_assure to identify when MLST JSON is empty. Added corresponding test

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• EC issue fix

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• Create a new JSON output file in input_assure

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Commits on Jun 14, 2024

• Ensure MLST JSON files from input_assure are gzipped

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• Merge pull request #13 from phac-nml/input_assure

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• Update samplesheet paths to mlst.json reports

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Commits on Jun 17, 2024

• Add gas parameter tests

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• Add test for hash-missing

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• Added test when counting missing data

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• Added test for removing missing loci

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• Added tests with pd_columns

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• Update documentation

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Commits on Jun 19, 2024

• Update CHANGELOG.md

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• Update workflow to allow gm_threshold to be single integers

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• Add success tests for different thresholds

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• Fix error in main_gm_threshold.nf.test

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Commits on Jun 20, 2024

• Merge pull request #15 from phac-nml/add_tests

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Commits on Jun 24, 2024

• Updating tests and documentation to correct 'scaled' distances

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• Added the expected test data files for scaled distances

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Commits on Jun 26, 2024

• Updated README to expand on GAS thresholds and linkage methods

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Commits on Jun 27, 2024

• Merge pull request #16 from phac-nml/update_scaled

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• Updating docs for release

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• Add link to release to CHANGELOG.md

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Commits on Jun 28, 2024

• Merge pull request #17 from phac-nml/release_version

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