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Add agat convertspgff2gtf #76

Merged
merged 26 commits into from
Jul 17, 2024
Merged

Add agat convertspgff2gtf #76

merged 26 commits into from
Jul 17, 2024

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Leila011
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@Leila011 Leila011 commented Jul 5, 2024 •
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Description

Issue ticket number

Closes #xxxx

Checklist before requesting a review

  • I have performed a self-review of my code

  • Conforms to the Contributing guidelines

  • Proposed changes are described in the CHANGELOG.md

  • I have tested my code with viash ns test --parallel -q <name or namespace>

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

rcannood
rcannood requested changes Jul 5, 2024
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Hey @Leila011 ! Thanks for creating this PR! I have some minor questions and suggestions ☺️

src/agat/agat_convertspgff2gtf/config.vsh.yaml Outdated Show resolved Hide resolved
src/agat/agat_convertspgff2gtf/config.vsh.yaml Outdated Show resolved Hide resolved
src/agat/agat_convertspgff2gtf/config.vsh.yaml Outdated Show resolved Hide resolved
src/agat/agat_convertspgff2gtf/test.sh Outdated Show resolved Hide resolved
src/agat/agat_convertspgff2gtf/test.sh Outdated

echo ">> Check if output is empty"
[ ! -s "output.gtf" ] && echo "Output file output.gtf is empty" && exit 1

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Can you also check the output's contents based on the input gff you provided?

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I added a test that extract the ID value from the first line of the GFF and then assess if the converted GTF first line contains the expected gene_id and ID. Let me know if this is not sufficient

@Leila011 Leila011 marked this pull request as ready for review July 9, 2024 09:03
@Leila011 Leila011 requested a review from rcannood July 9, 2024 09:03
rcannood
rcannood requested changes Jul 9, 2024
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minor changes requested ☺️

src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml Outdated Show resolved Hide resolved
src/agat/agat_convert_sp_gff2gtf/test.sh Show resolved Hide resolved
rcannood
rcannood approved these changes Jul 17, 2024
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LGTM! Thanks @Leila011 !

@rcannood rcannood merged commit 13c5439 into viash-hub:main Jul 17, 2024
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@rcannood rcannood rcannood approved these changes

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@Leila011 @rcannood