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fix: update CI workflow, snakemake wrappers and python / pandas code syntax #40

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fix: update CI workflow, snakemake wrappers and python / pandas code syntax #40

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Commits on Jun 6, 2023

  1. fix: stop using deprecated pd.read_table argument squeeze 

    Instead, use the `.squeeze("columns")` function, as for example done here:
https://github.com/sktime/sktime/pull/2693/files
    @dlaehnemann
    dlaehnemann authored Jun 6, 2023
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  2. update GitHub Actions workflow to use newer Actions versions

    @dlaehnemann
    dlaehnemann committed Jun 6, 2023
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  3. Merge branch 'update-ci' into fix-issue-39-read-table-squeeze-depreca… 

    …tion
    @dlaehnemann
    dlaehnemann committed Jun 6, 2023
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  4. snakefmt

    @dlaehnemann
    dlaehnemann committed Jun 6, 2023
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  5. update multiqc wrapper version

    @dlaehnemann
    dlaehnemann committed Jun 6, 2023
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Commits on Jun 7, 2023

  1. update all wrappers to latest version

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  2. adjust .gitignore for easier workflow development

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  3. adjust tabix index wrapper to new tabix wrapper substrucutre

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  4. adjust bwa index wrapper syntax to newer version

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  5. update syntax for newer picard markduplicates wrapper

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  6. update picard extra argument specification syntax

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  7. further picard argument parsing syntax update

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  8. explicitly specify sort order for picard markduplicates

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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  9. try --VALIDATION_STRINGENCY LENIENT for picard markduplicates

    @dlaehnemann
    dlaehnemann committed Jun 7, 2023
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Commits on Jun 8, 2023

  1. reintroduce --ASSUME_SORT_ORDER coordinate

    @dlaehnemann
    dlaehnemann committed Jun 8, 2023
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