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Overhaul strandedness detection / comparison #1306

Merged
merged 43 commits into from
Jun 19, 2024
Merged

Overhaul strandedness detection / comparison #1306

merged 43 commits into from
Jun 19, 2024

Commits on May 29, 2024

  1. Check RSeQC strandedness without reference to undetermined

    @pinin4fjords
    pinin4fjords committed May 29, 2024
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  2. Update subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf 

    Co-authored-by: Harshil Patel <[email protected]>
    @pinin4fjords @drpatelh
    pinin4fjords and drpatelh authored May 29, 2024
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Commits on Jun 12, 2024

  1. fix strand message

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    pinin4fjords committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. Merge branch 'dev' into improve_rseqc_strandedness

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    pinin4fjords committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. Update Salmon

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    pinin4fjords committed Jun 14, 2024
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  2. Add strandedness detection threshold parameter

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    pinin4fjords committed Jun 14, 2024
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  3. Add a consistent library type check between Salmon and RSeQC. Make th… 

    …e strand check results standard
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    pinin4fjords committed Jun 14, 2024
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  4. Amend for undetermined

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    pinin4fjords committed Jun 14, 2024
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  5. Constraint strand detection threshold

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    pinin4fjords committed Jun 14, 2024
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  6. Consistent defaults

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    pinin4fjords committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords authored Jun 17, 2024
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  2. Fix up after merge

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    pinin4fjords committed Jun 17, 2024
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  3. Fix for linting

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
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  4. update CHANGELOG

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    pinin4fjords committed Jun 17, 2024
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  5. Fix the fix

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
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  6. fix typos

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
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  7. [automated] Fix linting with Prettier

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    nf-core-bot committed Jun 17, 2024
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  8. Fix module lint error

    @pinin4fjords
    pinin4fjords committed Jun 17, 2024
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  9. revert config changed in error

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    pinin4fjords committed Jun 17, 2024
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  10. Merge branch 'improve_rseqc_strandedness' of github.com:nf-core/rnase… 

    …q into improve_rseqc_strandedness
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    pinin4fjords committed Jun 17, 2024
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  11. Fix conditionality

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    pinin4fjords committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. Clarify stranded/ unstraded at library level, include other library t… 

    …ypes in strand totals
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    pinin4fjords committed Jun 18, 2024
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  2. Allow for missing keys in salmon library counts for testing

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
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  3. Fix function tests

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    pinin4fjords committed Jun 18, 2024
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  4. Auto updating snapshot broke things for unaffected tests. So manually… 

    … insert snapshots from the only tests I do want to update
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    pinin4fjords committed Jun 18, 2024
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  5. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords authored Jun 18, 2024
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  6. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords authored Jun 18, 2024
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  7. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords authored Jun 18, 2024
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  8. Return percentages for strandedness

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
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  9. Explicitly publish lib_format_counts

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    pinin4fjords committed Jun 18, 2024
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  10. update docs

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
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  11. Fix typo

    @pinin4fjords
    pinin4fjords committed Jun 18, 2024
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  12. Prettier

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    pinin4fjords committed Jun 18, 2024
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  13. Fix typo 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @pinin4fjords @maxulysse
    pinin4fjords and maxulysse authored Jun 18, 2024
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Commits on Jun 19, 2024

  1. Set maximum on bars per column

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    pinin4fjords committed Jun 19, 2024
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  2. Pass/fail in separate mqc column

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    pinin4fjords committed Jun 19, 2024
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  3. Merge branch 'dev' into improve_rseqc_strandedness

    @pinin4fjords
    pinin4fjords authored Jun 19, 2024
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  4. Merge branch 'improve_rseqc_strandedness' of github.com:nf-core/rnase… 

    …q into improve_rseqc_strandedness
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    pinin4fjords committed Jun 19, 2024
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  5. Fix multiqc config for cell colors to highlight strandedness

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
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  6. Fix strand status conditional

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
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  7. update strand check image

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
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  8. Fix multiqc yaml

    @pinin4fjords
    pinin4fjords committed Jun 19, 2024
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  9. fix up params + usage

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    pinin4fjords committed Jun 19, 2024
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