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Implementation of KmerFinder subworkflow Custom Quast, and Custom MultiQC Reports #135

Merged
merged 62 commits into from
May 24, 2024
Merged

Implementation of KmerFinder subworkflow Custom Quast, and Custom MultiQC Reports #135

merged 62 commits into from
May 24, 2024

Commits on Nov 6, 2023

  1. add kmerfinder for shortreads

    @Daniel-VM
    Daniel-VM committed Nov 6, 2023
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  2. add module kmerfinder summary report

    @Daniel-VM
    Daniel-VM committed Nov 6, 2023
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Commits on Nov 14, 2023

  1. add module to find and download reference genome

    @Daniel-VM
    Daniel-VM committed Nov 14, 2023
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  2. fix kmerfinder summary input

    @Daniel-VM
    Daniel-VM committed Nov 14, 2023
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Commits on Nov 17, 2023

  1. update kmerfinder output file extension

    @Daniel-VM
    Daniel-VM committed Nov 17, 2023
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  2. add kmerfinder refseqid to meta

    @Daniel-VM
    Daniel-VM committed Nov 17, 2023
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  3. fix url in kmerfinder donwload ref

    @Daniel-VM
    Daniel-VM committed Nov 17, 2023
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  4. temporary commit

    @Daniel-VM
    Daniel-VM committed Nov 17, 2023
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Commits on Nov 19, 2023

  1. group assemblies by refseqid

    @Daniel-VM
    Daniel-VM committed Nov 19, 2023
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Commits on Nov 20, 2023

  1. allow global quast and by-refseqid quast

    @Daniel-VM
    Daniel-VM committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. move kmerfinder processing to subworkflow plus output refactoring

    @Daniel-VM
    Daniel-VM committed Nov 21, 2023
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  2. Merge branch 'bu-isciii_tmp' into buisciii-develop

    @Daniel-VM
    Daniel-VM committed Nov 21, 2023
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  3. allow quast to standard and byrefseq data

    @Daniel-VM
    Daniel-VM committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. add byrefseq quast reports to multiqc and patch quast

    @Daniel-VM
    Daniel-VM committed Nov 22, 2023
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Commits on Jan 2, 2024

  1. add byrefseq quast reports to multiqc and patch quast

    @Daniel-VM
    Daniel-VM committed Jan 2, 2024
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  2. update multiqc and append fastp metrics to assmebly metrics df

    @Daniel-VM
    Daniel-VM committed Jan 2, 2024
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  3. add new method to complie kmerfinder results into multiqc report

    @Daniel-VM
    Daniel-VM committed Jan 2, 2024
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  4. add long reads assembly metrics to custom multiqc

    @Daniel-VM
    Daniel-VM committed Jan 2, 2024
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  5. Merge branch 'buisciii-develop' of https://github.com/Daniel-VM/bacass … 

    …into buisciii-develop
    @Daniel-VM
    Daniel-VM committed Jan 2, 2024
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Commits on Jan 3, 2024

  1. fix custom multiqc when kmerfinder is not invoked

    @Daniel-VM
    Daniel-VM committed Jan 3, 2024
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Commits on Jan 4, 2024

  1. add custom multiqc for hybrid assembly

    @Daniel-VM
    Daniel-VM committed Jan 4, 2024
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  2. add file-check-exist and rename variables

    @Daniel-VM
    Daniel-VM committed Jan 4, 2024
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Commits on Jan 5, 2024

  1. update documentation and add save_trimmed option

    @Daniel-VM
    Daniel-VM committed Jan 5, 2024
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  2. add fastp additional options and fix input sample path

    @Daniel-VM
    Daniel-VM committed Jan 5, 2024
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Commits on Jan 15, 2024

  1. allow module to emit tsv report

    @Daniel-VM
    Daniel-VM committed Jan 15, 2024
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Commits on Feb 22, 2024

  1. add kmerfinder for shortreads

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  2. add module kmerfinder summary report

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  3. add module to find and download reference genome

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  4. fix kmerfinder summary input

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  5. update kmerfinder output file extension

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  6. add kmerfinder refseqid to meta

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  7. fix url in kmerfinder donwload ref

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  8. temporary commit

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  9. group assemblies by refseqid

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  10. allow global quast and by-refseqid quast

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  11. move kmerfinder processing to subworkflow plus output refactoring

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  12. allow quast to standard and byrefseq data

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  13. add byrefseq quast reports to multiqc and patch quast

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  14. update multiqc and append fastp metrics to assmebly metrics df

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  15. add new method to complie kmerfinder results into multiqc report

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  16. add long reads assembly metrics to custom multiqc

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  17. fix custom multiqc when kmerfinder is not invoked

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  18. add custom multiqc for hybrid assembly

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  19. add file-check-exist and rename variables

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  20. update documentation and add save_trimmed option

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  21. add fastp additional options and fix input sample path

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  22. allow module to emit tsv report

    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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  23. fix kmerFinder by narrowing down the reference genomes to a single wi… 

    …nning candidate
    @Daniel-VM
    Daniel-VM committed Feb 22, 2024
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Commits on Mar 19, 2024

  1. Fix divergen branches when mergin remote origin/buisciii-develop into… 

    … buisciii-develop
    @Daniel-VM
    Daniel-VM committed Mar 19, 2024
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Commits on May 17, 2024

  1. fix uncompress method to parse kmerfinder db

    @Daniel-VM
    Daniel-VM committed May 17, 2024
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  2. add new kmerfinderdb untar method and fix standalone py

    @Daniel-VM
    Daniel-VM committed May 17, 2024
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Commits on May 20, 2024

  1. fix step to prepare kmerfinderdb

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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  2. add kmerfinder to pipeline tests

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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  3. kmerfinder subworkflow cleaning

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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  4. Merge branch 'buisciii-develop' into dev

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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  5. remove unnecessary dependencies after merging branch

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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  6. fix linting after mergin branch

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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  7. update CHANGLEOG in nf-core#135

    @Daniel-VM
    Daniel-VM committed May 20, 2024
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Commits on May 23, 2024

  1. add reviewer suggestions nf-core#135 pt.1

    @Daniel-VM
    Daniel-VM committed May 23, 2024
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  2. fix multqc channels

    @Daniel-VM
    Daniel-VM committed May 23, 2024
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  3. add reviewer suggestions nf-core#135 pt.2

    @Daniel-VM
    Daniel-VM committed May 23, 2024
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  4. fix test_long_miniasm git CI test in nf-core#135

    @Daniel-VM
    Daniel-VM committed May 23, 2024
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