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nf-test quantify pseudoalignment #1246

Merged
merged 13 commits into from
Mar 12, 2024
Merged

nf-test quantify pseudoalignment #1246

merged 13 commits into from
Mar 12, 2024

Commits on Mar 8, 2024

  1. Add nf-test for quantify_psueudoalignment

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    adamrtalbot committed Mar 8, 2024
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  2. Some improvements but not working :(

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    adamrtalbot committed Mar 8, 2024
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  3. uncomment the comment

    @adamrtalbot
    adamrtalbot committed Mar 8, 2024
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  4. Swap to nf-core rnaseq test data (full path currently)

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    adamrtalbot committed Mar 8, 2024
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  5. Reference genome path mistake

    @adamrtalbot
    adamrtalbot committed Mar 8, 2024
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  6. Fix bugs in quantify_pseudoalignment 

    Fixes:
 - a single sample will now work and not raise an error when trying to parse the count data
 - duplicate transcripts now work with Salmon (previously it dropped one of them)
    @adamrtalbot
    adamrtalbot committed Mar 8, 2024
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  7. fixup

    @adamrtalbot
    adamrtalbot committed Mar 8, 2024
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  8. Update to use samplesheet in test-datasets repo

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    adamrtalbot committed Mar 8, 2024
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  9. Merge branch 'dev' into nf-test_quantify_pseudoalignment

    @adamrtalbot
    adamrtalbot committed Mar 8, 2024
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  10. Omit variable files from snap

    @adamrtalbot
    adamrtalbot committed Mar 8, 2024
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Commits on Mar 12, 2024

  1. SALMON tests keepDuplicates 

    Changes:
 - SALMON_INDEX will keep duplicates
 - summarizedexperiment will handle the missing transcripts
 - Version numbers checked in QUANTIFY_PSEUDO_ALIGNMENT subworkflow
    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
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  2. Merge branch 'dev' into nf-test_quantify_pseudoalignment

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
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  3. Merge branch 'dev' into nf-test_quantify_pseudoalignment

    @adamrtalbot
    adamrtalbot committed Mar 12, 2024
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