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Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1107

Merged
merged 48 commits into from
Nov 15, 2023
Merged

Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1107

merged 48 commits into from
Nov 15, 2023

Commits on Nov 7, 2023

  1. Add special GTF handling for stringtie

    @pinin4fjords
    pinin4fjords committed Nov 7, 2023
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  2. Update CHANGELOG

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    pinin4fjords committed Nov 7, 2023
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  3. appease eclint

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    pinin4fjords committed Nov 7, 2023
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  4. Comment dollar

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    pinin4fjords committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. Fix multiqc to avoid imp module error

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    pinin4fjords committed Nov 8, 2023
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Commits on Nov 9, 2023

  1. Actually, unify GTF filtering

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    pinin4fjords committed Nov 9, 2023
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  2. Reverse test profile change

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    pinin4fjords committed Nov 9, 2023
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  3. misc fixes

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    pinin4fjords committed Nov 9, 2023
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  4. Blackify

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    pinin4fjords committed Nov 9, 2023
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  5. move module to right path

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    pinin4fjords committed Nov 9, 2023
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  6. update changelog

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    pinin4fjords committed Nov 9, 2023
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  7. Correct selector

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    pinin4fjords committed Nov 9, 2023
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  8. Make gtf filtering dependent on gtf

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
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  9. Fix multiqc to avoid imp module error

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    pinin4fjords committed Nov 9, 2023
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  10. Fix transcript_id pattern

    @pinin4fjords
    pinin4fjords committed Nov 9, 2023
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  11. blackify

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    pinin4fjords committed Nov 9, 2023
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  12. emit chromosome-filtered gtf from genome preparation

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    pinin4fjords committed Nov 9, 2023
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  13. [skip ci] fix changelog

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    pinin4fjords committed Nov 9, 2023
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  14. Merge branch 'stringtie_gtf' of github.com:nf-core/rnaseq into string… 

    …tie_gtf
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    pinin4fjords committed Nov 9, 2023
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  15. Thank myself to poke CI

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    pinin4fjords committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. Merge branch 'stringtie_gtf' of github.com:nf-core/rnaseq into string… 

    …tie_gtf
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    pinin4fjords committed Nov 10, 2023
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  2. filter_gtf improvements

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    pinin4fjords committed Nov 10, 2023
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  3. Blackify

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    pinin4fjords committed Nov 10, 2023
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  4. [skip ci] Add resolved issues to changelog

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    pinin4fjords committed Nov 10, 2023
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  5. Merge branch 'dev' into stringtie_gtf

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    pinin4fjords committed Nov 10, 2023
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  6. Merge remote-tracking branch 'origin/dev' into stringtie_gtf

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    pinin4fjords committed Nov 10, 2023
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  7. reinstate publish modes

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    pinin4fjords committed Nov 10, 2023
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Commits on Nov 14, 2023

  1. [skip ci] Reduce logging in GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  2. [skip ci] Apply suggestions from code review 

    Co-authored-by: Matthias Zepper <[email protected]>
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    pinin4fjords and MatthiasZepper authored Nov 14, 2023
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  3. [skip ci] post-suggestion integration work

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    pinin4fjords committed Nov 14, 2023
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  4. [skip ci] more post-review tidy-up to GTF filtering script

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  5. [skip ci] reinstate logging

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  6. [skip ci] reinstate logging

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  7. [skip ci] Fix salmon subworkflow call for gtf

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  8. [skip ci] also raise value for no transcript ids

    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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  9. [skip ci] @drpatelh feedback: Try to avoid filtering process where no… 

    …t required
    @pinin4fjords
    pinin4fjords committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. Simplify GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 15, 2023
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  2. Blackify

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    pinin4fjords committed Nov 15, 2023
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  3. Document GTF filtering

    @pinin4fjords
    pinin4fjords committed Nov 15, 2023
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  4. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Nov 15, 2023
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  5. Merge branch 'dev' into stringtie_gtf

    @pinin4fjords
    pinin4fjords authored Nov 15, 2023
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  6. Bump modules config for merged module

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    pinin4fjords committed Nov 15, 2023
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  7. Bump pipeline version to 3.13.0

    @drpatelh
    drpatelh committed Nov 15, 2023
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  8. [skip ci] Changes from local review

    @drpatelh
    drpatelh committed Nov 15, 2023
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  9. Move --skip_* parameters to the same section

    @drpatelh
    drpatelh committed Nov 15, 2023
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  10. [skip ci] Tidy up code block

    @drpatelh
    drpatelh committed Nov 15, 2023
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  11. Move filter_gtf logic into main workflow

    @drpatelh
    drpatelh committed Nov 15, 2023
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  12. [automated] Fix linting with Prettier

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    nf-core-bot committed Nov 15, 2023
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