Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add mapping tools and viral pathogen List #21

Merged
merged 25 commits into from
Jul 22, 2024
Merged

Add mapping tools and viral pathogen List #21

merged 25 commits into from
Jul 22, 2024

Commits on Jun 18, 2024

  1. Add bowtie2 and minimap2 modules

    @LilyAnderssonLee
    LilyAnderssonLee committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    3b0328e View commit details
    Browse the repository at this point in the history

  2. ignore prettier check for viral_pathogen_List

    @LilyAnderssonLee
    LilyAnderssonLee committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    182fa6a View commit details
    Browse the repository at this point in the history

Commits on Jun 24, 2024

  1. update the pathogen list

    @LilyAnderssonLee
    LilyAnderssonLee committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    70fa463 View commit details
    Browse the repository at this point in the history

  2. Update .nf-core.yml 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jun 24, 2024
    Configuration menu
    Copy the full SHA
    25241c0 View commit details
    Browse the repository at this point in the history

  3. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jun 24, 2024
    Configuration menu
    Copy the full SHA
    87791e4 View commit details
    Browse the repository at this point in the history

  4. add test_taxid.config and rename the pathogen list name

    @LilyAnderssonLee
    LilyAnderssonLee committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    2788b9e View commit details
    Browse the repository at this point in the history

  5. update the test.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    aab25e2 View commit details
    Browse the repository at this point in the history

  6. add a new line to viralPahogenList.csv

    @LilyAnderssonLee
    LilyAnderssonLee committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    c065fe8 View commit details
    Browse the repository at this point in the history

Commits on Jul 10, 2024

  1. screen pathogens for short reads and update moduels of extractcentrif… 

    …ugereads and extractdiamondreads
    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    0ff8eed View commit details
    Browse the repository at this point in the history

  2. remove extra left-padding spaces in config/modules.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    59185ca View commit details
    Browse the repository at this point in the history

  3. add pathogen screening for long reads

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    003feba View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2024

  1. update the CHANGELOG

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 11, 2024
    Configuration menu
    Copy the full SHA
    2a7a354 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2024

  1. Update conf/modules.config 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    17e72b6 View commit details
    Browse the repository at this point in the history

  2. Update conf/modules.config 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    484429b View commit details
    Browse the repository at this point in the history

  3. Update conf/modules.config 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    22aa86a View commit details
    Browse the repository at this point in the history

  4. Update conf/modules.config 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    6a5e515 View commit details
    Browse the repository at this point in the history

  5. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    3b912c7 View commit details
    Browse the repository at this point in the history

  6. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    b19db4f View commit details
    Browse the repository at this point in the history

  7. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    7b1b179 View commit details
    Browse the repository at this point in the history

  8. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    c2cc381 View commit details
    Browse the repository at this point in the history

  9. Trail whitespace

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    eac76ca View commit details
    Browse the repository at this point in the history

  10. move the multiqc to the end of modules.config

    @LilyAnderssonLee
    LilyAnderssonLee committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    bed5faa View commit details
    Browse the repository at this point in the history

  11. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    d16c390 View commit details
    Browse the repository at this point in the history

  12. Update nextflow.config 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    36cc422 View commit details
    Browse the repository at this point in the history

  13. Update nextflow_schema.json 

    Co-authored-by: Sofia Stamouli <[email protected]>
    @LilyAnderssonLee @sofstam
    LilyAnderssonLee and sofstam authored Jul 18, 2024
    Configuration menu
    Copy the full SHA
    9346870 View commit details
    Browse the repository at this point in the history