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Update/input assure to accommodate changes in locidex mlst.json allele reports #28

Merged
merged 20 commits into from
Aug 21, 2024
Merged

Update/input assure to accommodate changes in locidex mlst.json allele reports #28

merged 20 commits into from
Aug 21, 2024

Commits on Aug 15, 2024

  1. Update locidex container registry

    @kylacochrane
    kylacochrane committed Aug 15, 2024
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  2. Update input_assure.py to accomodate the revised Locidex mlst.json re… 

    …port format
    @kylacochrane
    kylacochrane committed Aug 15, 2024
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  3. Update test data (reports and samplesheets) to accomodate the revised… 

    … Locidex mlst.json report format
    @kylacochrane
    kylacochrane committed Aug 15, 2024
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  4. Update paths to mlst files in samplesheet.csv

    @kylacochrane
    kylacochrane committed Aug 15, 2024
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  5. Fixed error in samplesheet

    @kylacochrane
    kylacochrane committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Fixed typo

    @kylacochrane
    kylacochrane committed Aug 16, 2024
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Commits on Aug 19, 2024

  1. Updated container registry handling

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  2. add user UID/GID to Nextflow Docker run in CI to fix getpwuid() error

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  3. add root user to Nextflow Docker run in CI to fix getpwuid() error

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  4. Updated container for arborview

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  5. Refactor user configuration for locidex module: Remove --user specs f… 

    …rom ci.yml and add to modules.conf
    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  6. Revert to previous user config in ci.yml

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  7. Update --user in ci.yml

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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  8. Removed --user configurations for locidex

    @kylacochrane
    kylacochrane committed Aug 19, 2024
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Commits on Aug 20, 2024

  1. Updated CHANGELOG.md

    @kylacochrane
    kylacochrane committed Aug 20, 2024
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  2. Updated release version

    @kylacochrane
    kylacochrane committed Aug 20, 2024
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  3. Removed print debugging statement in input_assure.py

    @kylacochrane
    kylacochrane committed Aug 20, 2024
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  4. Replace unsorted list with sorted() for consistent ordering in input_… 

    …assure.py
    @kylacochrane
    kylacochrane committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. Update locidex to version 0.2.3

    @kylacochrane
    kylacochrane committed Aug 21, 2024
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  2. Add link to release tag

    @kylacochrane
    kylacochrane committed Aug 21, 2024
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