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Adding stubs at all level #1335

Merged
merged 42 commits into from
Aug 21, 2024
Merged

Adding stubs at all level #1335

merged 42 commits into from
Aug 21, 2024

Commits on Jul 3, 2024

  1. stub for align_star + a single snapshot match per test

    @maxulysse
    maxulysse committed Jul 3, 2024
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  2. add stubs + code polish + Harshil align

    @maxulysse
    maxulysse committed Jul 3, 2024
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  3. add stub

    @maxulysse
    maxulysse committed Jul 3, 2024
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  4. update all nf-core modules and subworkflows and do not include tags

    @maxulysse
    maxulysse committed Jul 3, 2024
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  5. simplify snapshot for stub

    @maxulysse
    maxulysse committed Jul 3, 2024
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  6. add stubs for subworkflow local quantify_rsem

    @maxulysse
    maxulysse committed Jul 3, 2024
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  7. update default snapshot

    @maxulysse
    maxulysse committed Jul 3, 2024
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Commits on Jul 4, 2024

  1. add plugin

    @maxulysse
    maxulysse committed Jul 4, 2024
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  2. update all subworkflows

    @maxulysse
    maxulysse committed Jul 4, 2024
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  3. do not snapshot fastq in stub

    @maxulysse
    maxulysse committed Jul 4, 2024
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  4. pipeline level stub

    @maxulysse
    maxulysse committed Jul 4, 2024
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  5. fix stub test for prepare_genome

    @maxulysse
    maxulysse committed Jul 4, 2024
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  6. update all subworkflows

    @maxulysse
    maxulysse committed Jul 4, 2024
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Commits on Jul 5, 2024

  1. correctly align

    @maxulysse
    maxulysse committed Jul 5, 2024
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Commits on Jul 9, 2024

  1. update all modules

    @maxulysse
    maxulysse committed Jul 9, 2024
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Commits on Jul 11, 2024

  1. use seqera containers

    @maxulysse
    maxulysse committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Jul 12, 2024
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  2. update all modules/subworkflows + remove tags

    @maxulysse
    maxulysse committed Jul 12, 2024
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  3. update snapshot

    @maxulysse
    maxulysse committed Jul 12, 2024
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Commits on Jul 16, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Jul 16, 2024
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Commits on Jul 22, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Jul 22, 2024
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  2. update nf-test to 0.9.0

    @maxulysse
    maxulysse committed Jul 22, 2024
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  3. sort

    @maxulysse
    maxulysse committed Jul 22, 2024
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  4. update all modules/subworkflows + remove tags

    @maxulysse
    maxulysse committed Jul 22, 2024
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  5. remove tags

    @maxulysse
    maxulysse committed Jul 22, 2024
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  6. keep card 3.1.1 that does not break CI due to weird RG

    @maxulysse
    maxulysse committed Jul 22, 2024
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  7. update snapshot

    @maxulysse
    maxulysse committed Jul 22, 2024
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  8. update snapshot

    @maxulysse
    maxulysse committed Jul 22, 2024
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  9. update all modules + subworkflows / remove tags + path markduplicates

    @maxulysse
    maxulysse committed Jul 22, 2024
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  10. update snapshots

    @maxulysse
    maxulysse committed Jul 22, 2024
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  11. update stringtie_stringtie

    @maxulysse
    maxulysse committed Jul 22, 2024
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  12. update snapshots for fastq_align_hisat2

    @maxulysse
    maxulysse committed Jul 22, 2024
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  13. add proper stubs and tests for local star_*_igenomes modules

    @maxulysse
    maxulysse committed Jul 22, 2024
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Commits on Aug 16, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Aug 16, 2024
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  2. proper sha for module bedtools/genomecov

    @maxulysse
    maxulysse committed Aug 16, 2024
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  3. update samtools/stats module + rm tags

    @maxulysse
    maxulysse committed Aug 16, 2024
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Commits on Aug 20, 2024

  1. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Aug 20, 2024
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  2. clean up stub tests

    @maxulysse
    maxulysse committed Aug 20, 2024
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  3. Merge branch 'dev' into stubs_everywhere

    @maxulysse
    maxulysse committed Aug 20, 2024
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  4. update CHANGELOG

    @maxulysse
    maxulysse committed Aug 20, 2024
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  5. update snapshot

    @maxulysse
    maxulysse committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. update snapshot

    @maxulysse
    maxulysse committed Aug 21, 2024
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