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feat: Goleft indexcov #2734

Merged
merged 61 commits into from
May 7, 2024
Merged

feat: Goleft indexcov #2734

merged 61 commits into from
May 7, 2024

Commits on Sep 21, 2020

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Commits on Nov 9, 2020

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

    tdayris committed Nov 9, 2020
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Commits on Jul 2, 2021

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Commits on Jul 16, 2021

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

    tdayris committed Jul 16, 2021
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Commits on Apr 29, 2022

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Commits on May 13, 2022

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Commits on Jun 27, 2022

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Commits on Oct 11, 2022

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

    tdayris committed Oct 11, 2022
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Commits on Oct 13, 2022

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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  23. fix: set RG tag (snakemake#593)

    FelixMoelder authored and tdayris committed Oct 13, 2022
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  24. Update conventional-prs.yml

    johanneskoester authored and tdayris committed Oct 13, 2022
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  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
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  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
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Commits on Dec 5, 2022

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    tdayris committed Dec 5, 2022
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Commits on Mar 31, 2023

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    tdayris committed Mar 31, 2023
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Commits on Apr 7, 2023

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

    tdayris committed Apr 7, 2023
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Commits on Apr 11, 2023

  1. revert

    tdayris committed Apr 11, 2023
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Commits on Apr 14, 2023

  1. revert

    tdayris committed Apr 14, 2023
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Commits on May 2, 2023

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    tdayris committed May 2, 2023
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Commits on Jun 14, 2023

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Commits on Jul 11, 2023

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

    tdayris committed Jul 11, 2023
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Commits on Jul 26, 2023

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

    tdayris committed Jul 26, 2023
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Commits on Aug 9, 2023

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

    tdayris committed Aug 9, 2023
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Commits on Aug 11, 2023

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

    tdayris committed Aug 11, 2023
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Commits on Nov 24, 2023

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Commits on Feb 28, 2024

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Commits on Mar 6, 2024

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Commits on Mar 11, 2024

  1. initial commit

    tdayris committed Mar 11, 2024
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  2. pin & clean

    tdayris committed Mar 11, 2024
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  3. Update bio/goleft/indexcov/wrapper.py

    Co-authored-by: Filipe G. Vieira <[email protected]>
    tdayris and fgvieira authored Mar 11, 2024
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Commits on Mar 12, 2024

  1. Conding scheme

    tdayris committed Mar 12, 2024
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  2. no longer creating out dir

    tdayris committed Mar 12, 2024
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  3. re-include mkdir

    tdayris committed Mar 12, 2024
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Commits on Mar 14, 2024

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Commits on May 7, 2024

  1. Update bio/goleft/indexcov/wrapper.py

    Co-authored-by: Filipe G. Vieira <[email protected]>
    tdayris and fgvieira authored May 7, 2024
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  2. black

    tdayris committed May 7, 2024
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