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

New tool: biobambam/bamsormadup #1478

Merged
merged 27 commits into from
Apr 6, 2022
Merged

New tool: biobambam/bamsormadup #1478

merged 27 commits into from
Apr 6, 2022

Commits on Apr 1, 2022

  1. add bamsormadup

    @matthdsm
    matthdsm committed Apr 1, 2022
    Configuration menu
    Copy the full SHA
    453a13c View commit details
    Browse the repository at this point in the history

  2. fix yaml

    @matthdsm
    matthdsm committed Apr 1, 2022
    Configuration menu
    Copy the full SHA
    7fc5834 View commit details
    Browse the repository at this point in the history

  3. add test.yml

    @matthdsm
    matthdsm committed Apr 1, 2022
    Configuration menu
    Copy the full SHA
    596afb3 View commit details
    Browse the repository at this point in the history

Commits on Apr 4, 2022

  1. Update tests/modules/biobambam/bamsormadup/test.yml 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @matthdsm @jfy133
    matthdsm and jfy133 committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    dc2b038 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into tool/bamsormadup

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    e8e2674 View commit details
    Browse the repository at this point in the history

  3. test meta.yaml: remove md5sums

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    1e3ee75 View commit details
    Browse the repository at this point in the history

  4. Tool bamsormadup: 

    - add (optional) reference input
- add bam index ouput
- add cram output option
- make metrics output: more general
    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    4908f1e View commit details
    Browse the repository at this point in the history

  5. Merge branch 'master' into tool/bamsormadup

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    4b1d7cb View commit details
    Browse the repository at this point in the history

  6. fix input and output formats

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    6c338a1 View commit details
    Browse the repository at this point in the history

  7. update input file description

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    bf015bb View commit details
    Browse the repository at this point in the history

  8. drop sam output, goes against nf-core regs; add input check for cram … 

    …files
    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    b97ebb9 View commit details
    Browse the repository at this point in the history

  9. fix typo

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    b936a5d View commit details
    Browse the repository at this point in the history

  10. Merge branch 'master' into tool/bamsormadup

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    2d6231a View commit details
    Browse the repository at this point in the history

  11. Update modules/biobambam/bamsormadup/main.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @matthdsm @jfy133
    matthdsm and jfy133 committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    bac3951 View commit details
    Browse the repository at this point in the history

  12. improve ref fasta name

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    be386c8 View commit details
    Browse the repository at this point in the history

  13. fix if else shorthand

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    156a9ab View commit details
    Browse the repository at this point in the history

  14. fix syntax error

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    96b4460 View commit details
    Browse the repository at this point in the history

  15. kind of fix tests

    @matthdsm
    matthdsm committed Apr 4, 2022
    Configuration menu
    Copy the full SHA
    baead3c View commit details
    Browse the repository at this point in the history

Commits on Apr 5, 2022

  1. Merge branch 'master' into tool/bamsormadup

    @matthdsm
    matthdsm committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    e609147 View commit details
    Browse the repository at this point in the history

  2. set fixed suffix for metrics file to keep it in line with picard and … 

    …bammarkduplicates2
    @matthdsm
    matthdsm committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    ed379a8 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'master' into tool/bamsormadup

    @matthdsm
    matthdsm committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    cd5fd67 View commit details
    Browse the repository at this point in the history

  4. fix command line

    @matthdsm
    matthdsm committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    50b835b View commit details
    Browse the repository at this point in the history

  5. update test.yml

    @matthdsm
    matthdsm committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    78ee44a View commit details
    Browse the repository at this point in the history

  6. add support for multiple input bams

    @matthdsm
    matthdsm committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    389c804 View commit details
    Browse the repository at this point in the history

Commits on Apr 6, 2022

  1. Update modules/biobambam/bamsormadup/meta.yml 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @matthdsm @jfy133
    matthdsm and jfy133 committed Apr 6, 2022
    Configuration menu
    Copy the full SHA
    a788720 View commit details
    Browse the repository at this point in the history

  2. Update modules/biobambam/bamsormadup/meta.yml 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @matthdsm @jfy133
    matthdsm and jfy133 committed Apr 6, 2022
    Configuration menu
    Copy the full SHA
    269eedc View commit details
    Browse the repository at this point in the history

  3. Update tests/modules/biobambam/bamsormadup/test.yml 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @matthdsm @jfy133
    matthdsm and jfy133 committed Apr 6, 2022
    Configuration menu
    Copy the full SHA
    9c88514 View commit details
    Browse the repository at this point in the history