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Bugfix/several runtime issues #46

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Bugfix/several runtime issues #46

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Commits on Apr 16, 2024

  1. Merge pull request #24 from EBI-Metagenomics/dev 

    Dev
    @tgurbich
    tgurbich authored Apr 16, 2024
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Commits on Jun 5, 2024

  1. Merge pull request #33 from EBI-Metagenomics/dev 

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    @tgurbich
    tgurbich authored Jun 5, 2024
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Commits on Jul 2, 2024

  1. Merge pull request #36 from EBI-Metagenomics/dev 

    Dev
    @tgurbich
    tgurbich authored Jul 2, 2024
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Commits on Jul 12, 2024

  1. Merge pull request #37 from EBI-Metagenomics/dev 

    Added citation
    @tgurbich
    tgurbich authored Jul 12, 2024
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Commits on Jul 19, 2024

  1. Merge pull request #41 from EBI-Metagenomics/bugfix/38-unifire-mount-… 

    …docker

Unifre mount issue with docker.
    @mberacochea
    mberacochea authored Jul 19, 2024
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Commits on Jul 23, 2024

  1. Merge pull request #43 from EBI-Metagenomics/dev 

    Dev -> main for release v1.3
    @mberacochea
    mberacochea authored Jul 23, 2024
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Commits on Sep 26, 2024

  1. A few patches for prokka, ips, detect_trna, crisprcasfinder and amrfi… 

    …nder.

These tools are very picky with the tmp directory, so I've implemented a workaround
using a "tmp" directory in the process workdir.
    @mberacochea
    mberacochea committed Sep 26, 2024
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  2. Wrong character to comment a line in bash :(

    @mberacochea
    mberacochea committed Sep 26, 2024
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  3. Unifire - apptainer mount fix

    @mberacochea
    mberacochea committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. Minor change on tmp creation on prokka and amrfinder (mkdir -p.. just… 

    … in case)
    @mberacochea
    mberacochea committed Sep 27, 2024
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  2. Several changes to improve the code base and python tests 

    - Removed the custom python container with a seqera container one (retry and requests)
- Removed the custom python container with the biocontainers python one when possible
- Added the singularity image to the containers on those modules that was possible
- Added ruff, black and some other base pre-commit
- Migrated the python unit tests to pytest and fixed them
- Ran ruff and black on the scripts

I am testing all this ATM.
    @mberacochea
    mberacochea committed Sep 27, 2024
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  3. Fix python linting issues / correct container on annotate_gff.nf

    @mberacochea
    mberacochea committed Sep 27, 2024
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  4. Re-format all the files with the linters

    @mberacochea
    mberacochea committed Sep 27, 2024
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  5. Fix pytest setup

    @mberacochea
    mberacochea committed Sep 27, 2024
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  6. Bump actions and code from py3.8 to 3.9

    @mberacochea
    mberacochea committed Sep 27, 2024
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  7. Update the git ignore, and push the tests data folder

    @mberacochea
    mberacochea committed Sep 27, 2024
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  8. Added the HD profile (was missing from nextflow.config)

    @mberacochea
    mberacochea committed Sep 27, 2024
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  9. Fix nf-core linting - set to ignore the .gitignore files 

    Our .gitignore is more comprehensive than the nf-core template one
    @mberacochea
    mberacochea committed Sep 27, 2024
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  10. Adjust the scratch dir for the embl_hd profile

    @mberacochea
    mberacochea committed Sep 27, 2024
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  11. Disable "scratch" for EMBL HD.

    @mberacochea
    mberacochea committed Sep 27, 2024
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Commits on Oct 9, 2024

  1. singularity_cachedir as a parameter

    @mberacochea
    mberacochea committed Oct 9, 2024
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  2. Adjusted the configs a bit

    @mberacochea
    mberacochea committed Oct 9, 2024
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  3. Freeze nf-core tools to 2.14.1 until the liniting in fixed for versio… 

    …n >= 3
    @mberacochea
    mberacochea committed Oct 9, 2024
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Commits on Nov 12, 2024

  1. Fix typo in embl_hd configuration file

    @mberacochea
    mberacochea committed Nov 12, 2024
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