8000 Find test dataset where PRESEQ doesn't fail · Issue #276 · nf-core/chipseq · GitHub
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Find test dataset where PRESEQ doesn't fail #276

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Find test dataset where PRESEQ doesn't fail#276
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JoseEspinosa
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enhancement
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2.3

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@drpatelh
drpatelh
opened on May 9, 2022

Related to nf-core/rnaseq#544

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  1. drpatelh
    added
    enhancement
    on May 9, 2022
  2. JoseEspinosa
    self-assigned this
    on May 9, 2022

  3. JoseEspinosa commented on May 12, 2022

    @JoseEspinosa
    JoseEspinosa
    on May 12, 2022
    Member

    I tried with the same files of the current test dataset:

    SRR1822153
SRR1822154
SRR1822157
SRR1822158
SRR5204809
SRR5204810

    And the same approach you used for the rnaseq pipeline (filtering ChrI using viralrecon) not even subsampling the resulting fastq files. With this data PRESEQ still failed for one of the control samples (SRR5204810) 😞
    So, I guess we will have to come up with a different dataset, or do you have any other suggestions @drpatelh ?

  4. JoseEspinosa
    added this to the 2.1 milestone on Aug 5, 2022
  5. JoseEspinosa
    modified the milestones: 2.1, 2.2 on Jul 24, 2024
  6. Kevin-Brockers
    modified the milestones: 2.2, 2.3-enhancements on Apr 1, 2026

  7. Kevin-Brockers commented on Apr 1, 2026

    @Kevin-Brockers
    Kevin-Brockers
    on Apr 1, 2026

    Isn't preseq now disabled by default? See: #455
    Wouldn't be the nature of preseq failing with the small test data used?

    Not sure if it's worth to include tests for it only when run on the full data set tests?

    I remove it from the 2.2 milestones and assign it for a potential 2.3 release

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