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.

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

feat: Bwameth index #3162

Merged
merged 62 commits into from
Aug 30, 2024
Merged

feat: Bwameth index #3162

merged 62 commits into from
Aug 30, 2024

Commits on Sep 21, 2020

  1. Configuration menu
    Copy the full SHA
    ab82604 View commit details
    Browse the repository at this point in the history

Commits on Nov 9, 2020

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Nov 9, 2020
    Configuration menu
    Copy the full SHA
    de77ade View commit details
    Browse the repository at this point in the history

Commits on Jul 2, 2021

  1. Configuration menu
    Copy the full SHA
    9b1447e View commit details
    Browse the repository at this point in the history

Commits on Jul 16, 2021

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Jul 16, 2021
    Configuration menu
    Copy the full SHA
    91fd32d View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    ed2a885 View commit details
    Browse the repository at this point in the history

Commits on Apr 29, 2022

  1. Configuration menu
    Copy the full SHA
    2a1655b View commit details
    Browse the repository at this point in the history

Commits on May 13, 2022

  1. Configuration menu
    Copy the full SHA
    044cf8a View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2022

  1. Configuration menu
    Copy the full SHA
    5b1c7b4 View commit details
    Browse the repository at this point in the history

Commits on Oct 11, 2022

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Oct 11, 2022
    Configuration menu
    Copy the full SHA
    aea600e View commit details
    Browse the repository at this point in the history

Commits on Oct 13, 2022

  1. Configuration menu
    Copy the full SHA
    ac4ac81 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    88c479c View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    8d92bb5 View commit details
    Browse the repository at this point in the history
  4. perf: autobump bio/bcftools/index/environment.yaml (snakemake#570)

    * perf: update bio/bcftools/index/environment.yaml.
    
    * perf: update bio/bcftools/index/environment.yaml.
    
    * perf: update bio/bcftools/index/environment.yaml.
    johanneskoester authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    1c444dc View commit details
    Browse the repository at this point in the history
  5. chore: release 1.15.1 (snakemake#569)

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    github-actions[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    534f834 View commit details
    Browse the repository at this point in the history
  6. perf: update bio/bgzip/environment.yaml. (snakemake#577)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    7eb277c View commit details
    Browse the repository at this point in the history
  7. perf: update bio/bellerophon/environment.yaml. (snakemake#576)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    63f8acb View commit details
    Browse the repository at this point in the history
  8. perf: update bio/assembly-stats/environment.yaml. (snakemake#575)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    963bedf View commit details
    Browse the repository at this point in the history
  9. perf: update bio/adapterremoval/environment.yaml. (snakemake#573)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    ff74710 View commit details
    Browse the repository at this point in the history
  10. chore: autobump conda envs (snakemake#571)

    * Add autobump action
    
    * fix paths
    
    * dbg
    
    * dbg branch
    
    * add checkout
    
    * dbg
    
    * trigger rerun
    
    * entity regex and add label
    
    * dbg
    
    * Update autobump.yml
    
    * Update autobump.yml
    johanneskoester authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    bb60c16 View commit details
    Browse the repository at this point in the history
  11. perf: update bio/delly/environment.yaml. (snakemake#584)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    d9a7a6a View commit details
    Browse the repository at this point in the history
  12. perf: update bio/busco/environment.yaml. (snakemake#581)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    e0220d2 View commit details
    Browse the repository at this point in the history
  13. perf: update bio/clustalo/environment.yaml. (snakemake#582)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    ae10993 View commit details
    Browse the repository at this point in the history
  14. perf: update bio/fastp/environment.yaml. (snakemake#585)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    76c9845 View commit details
    Browse the repository at this point in the history
  15. perf: update bio/fastq_screen/environment.yaml. (snakemake#586)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    853a36d View commit details
    Browse the repository at this point in the history
  16. perf: update bio/fasttree/environment.yaml. (snakemake#588)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    576c54a View commit details
    Browse the repository at this point in the history
  17. perf: update bio/fastqc/environment.yaml. (snakemake#587)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    e473ff7 View commit details
    Browse the repository at this point in the history
  18. perf: update bio/filtlong/environment.yaml. (snakemake#589)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    6f5f48f View commit details
    Browse the repository at this point in the history
  19. perf: update bio/freebayes/environment.yaml. (snakemake#590)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    5a1f598 View commit details
    Browse the repository at this point in the history
  20. perf: update bio/genefuse/environment.yaml. (snakemake#591)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    f60db66 View commit details
    Browse the repository at this point in the history
  21. perf: update bio/genomepy/environment.yaml. (snakemake#592)

    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    snakedeploy-bot[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    cb6b616 View commit details
    Browse the repository at this point in the history
  22. chore: release 1.15.2 (snakemake#578)

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    github-actions[bot] authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    f618f0d View commit details
    Browse the repository at this point in the history
  23. fix: set RG tag (snakemake#593)

    FelixMoelder authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    141e09e View commit details
    Browse the repository at this point in the history
  24. Update conventional-prs.yml

    johanneskoester authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    278f508 View commit details
    Browse the repository at this point in the history
  25. perf: autobump bio/deepvariant (snakemake#583)

    Automatic update of bio/deepvariant.
    
    Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
    Co-authored-by: Johannes Köster <[email protected]>
    2 people authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    de6ce85 View commit details
    Browse the repository at this point in the history
  26. feat: bazam wrapper (snakemake#580)

    <!-- Ensure that the PR title follows conventional commit style (<type>:
    <description>)-->
    <!-- Possible types are here:
    https://github.com/commitizen/conventional-commit-types/blob/master/index.json
    -->
    
    ### Description
    
    <!-- Add a description of your PR here-->
    
    ### QC
    <!-- Make sure that you can tick the boxes below. -->
    
    * [x] I confirm that:
    
    For all wrappers added by this PR, 
    
    * there is a test case which covers any introduced changes,
    * `input:` and `output:` file paths in the resulting rule can be changed
    arbitrarily,
    * either the wrapper can only use a single core, or the example rule
    contains a `threads: x` statement with `x` being a reasonable default,
    * rule names in the test case are in
    [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
    what the rule is about or match the tools purpose or name (e.g.,
    `map_reads` for a step that maps reads),
    * all `environment.yaml` specifications follow [the respective best
    practices](https://stackoverflow.com/a/64594513/2352071),
    * wherever possible, command line arguments are inferred and set
    automatically (e.g. based on file extensions in `input:` or `output:`),
    * all fields of the example rules in the `Snakefile`s and their entries
    are explained via comments (`input:`/`output:`/`params:` etc.),
    * `stderr` and/or `stdout` are logged correctly (`log:`), depending on
    the wrapped tool,
    * temporary files are either written to a unique hidden folder in the
    working directory, or (better) stored where the Python function
    `tempfile.gettempdir()` points to (see
    [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
    this also means that using any Python `tempfile` default behavior
    works),
    * the `meta.yaml` contains a link to the documentation of the respective
    tool or command,
    * `Snakefile`s pass the linting (`snakemake --lint`),
    * `Snakefile`s are formatted with
    [snakefmt](https://github.com/snakemake/snakefmt),
    * Python wrapper scripts are formatted with
    [black](https://black.readthedocs.io).
    * Conda environments use a minimal amount of channels, in recommended
    ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
    conda-forge should have highest priority and defaults channels are
    usually not needed because most packages are in conda-forge nowadays).
    christopher-schroeder authored and tdayris committed Oct 13, 2022
    Configuration menu
    Copy the full SHA
    f9332c2 View commit details
    Browse the repository at this point in the history
  27. Configuration menu
    Copy the full SHA
    39c488d View commit details
    Browse the repository at this point in the history

Commits on Dec 5, 2022

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Dec 5, 2022
    Configuration menu
    Copy the full SHA
    d1a68e5 View commit details
    Browse the repository at this point in the history

Commits on Mar 31, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Mar 31, 2023
    Configuration menu
    Copy the full SHA
    7aadebb View commit details
    Browse the repository at this point in the history

Commits on Apr 7, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Apr 7, 2023
    Configuration menu
    Copy the full SHA
    6878cd6 View commit details
    Browse the repository at this point in the history

Commits on Apr 11, 2023

  1. revert

    tdayris committed Apr 11, 2023
    Configuration menu
    Copy the full SHA
    77a2f4c View commit details
    Browse the repository at this point in the history

Commits on Apr 14, 2023

  1. revert

    tdayris committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    939082e View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    91ec8ee View commit details
    Browse the repository at this point in the history

Commits on May 2, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed May 2, 2023
    Configuration menu
    Copy the full SHA
    90518cf View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2023

  1. Configuration menu
    Copy the full SHA
    bfdc5e0 View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Jul 11, 2023
    Configuration menu
    Copy the full SHA
    51730a3 View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Jul 26, 2023
    Configuration menu
    Copy the full SHA
    537693b View commit details
    Browse the repository at this point in the history

Commits on Aug 9, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Aug 9, 2023
    Configuration menu
    Copy the full SHA
    8e9f3ab View commit details
    Browse the repository at this point in the history

Commits on Aug 11, 2023

  1. Merge remote-tracking branch 'upstream/master'

    tdayris committed Aug 11, 2023
    Configuration menu
    Copy the full SHA
    55e063c View commit details
    Browse the repository at this point in the history

Commits on Nov 24, 2023

  1. Configuration menu
    Copy the full SHA
    aae0451 View commit details
    Browse the repository at this point in the history

Commits on Feb 28, 2024

  1. Configuration menu
    Copy the full SHA
    4c0c2dc View commit details
    Browse the repository at this point in the history

Commits on Mar 6, 2024

  1. Configuration menu
    Copy the full SHA
    e655c03 View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2024

  1. Configuration menu
    Copy the full SHA
    9368db6 View commit details
    Browse the repository at this point in the history

Commits on Jul 16, 2024

  1. Configuration menu
    Copy the full SHA
    20f5129 View commit details
    Browse the repository at this point in the history

Commits on Aug 26, 2024

  1. Configuration menu
    Copy the full SHA
    a19d670 View commit details
    Browse the repository at this point in the history

Commits on Aug 27, 2024

  1. feat: bwameth index

    tdayris committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    eaf34e5 View commit details
    Browse the repository at this point in the history

Commits on Aug 30, 2024

  1. Aligner autodetection

    tdayris committed Aug 30, 2024
    Configuration menu
    Copy the full SHA
    e8ad777 View commit details
    Browse the repository at this point in the history
  2. Black

    tdayris committed Aug 30, 2024
    Configuration menu
    Copy the full SHA
    2aefa9e View commit details
    Browse the repository at this point in the history
  3. black

    tdayris committed Aug 30, 2024
    Configuration menu
    Copy the full SHA
    ec78fd9 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    4cf32d1 View commit details
    Browse the repository at this point in the history
  5. Update bio/bwameth/index/meta.yaml

    Co-authored-by: Filipe G. Vieira <[email protected]>
    tdayris and fgvieira authored Aug 30, 2024
    Configuration menu
    Copy the full SHA
    9338e8b View commit details
    Browse the repository at this point in the history
  6. Change prefix and ensure out_dir is not empty

    tdayris committed Aug 30, 2024
    Configuration menu
    Copy the full SHA
    677c9e4 View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    b0a25cb View commit details
    Browse the repository at this point in the history