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Skyline transfer #36

Merged
merged 31 commits into from
Feb 8, 2024
Merged

Skyline transfer #36

merged 31 commits into from
Feb 8, 2024

Commits on Feb 1, 2024

  1. fix: align mg assembly rules to expected outputs

    Ryan Routsong committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. fix: sample sheet processing and run id searching fixes from bigsky t… 

    …esting
    @rroutsong
    rroutsong committed Feb 2, 2024
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  2. fix: update resource config for bcl2fastq

    @rroutsong
    rroutsong committed Feb 2, 2024
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  3. feat: add execution context documentation

    @rroutsong
    rroutsong committed Feb 2, 2024
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  4. feat: add execution docs to nav

    @rroutsong
    rroutsong committed Feb 2, 2024
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  5. fix: update execution docs for sbatch execution on biowulf

    @rroutsong
    rroutsong committed Feb 2, 2024
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  6. fix: temporarily use branch version of profiles

    @rroutsong
    rroutsong committed Feb 2, 2024
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  7. feat: update execution documentation

    @rroutsong
    rroutsong committed Feb 2, 2024
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  8. fix: update regex for miseq run id compatibility

    @rroutsong
    rroutsong committed Feb 2, 2024
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  9. fix: update miseq regex use . instead of \N

    @rroutsong
    rroutsong committed Feb 2, 2024
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Commits on Feb 5, 2024

  1. fix: don't error if progressbar is not installed

    @rroutsong
    rroutsong committed Feb 5, 2024
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  2. fix: process different read indicators in the sample sheet

    @rroutsong
    rroutsong committed Feb 5, 2024
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  3. fix: clean up requirements

    @rroutsong
    rroutsong committed Feb 5, 2024
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  4. fix: update profiles

    @rroutsong
    rroutsong committed Feb 5, 2024
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  5. fix: fix cpu allocation bug, make it only possible to get 2 cpus per … 

    …task
    @rroutsong
    rroutsong committed Feb 5, 2024
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Commits on Feb 6, 2024

  1. fix: close sample sheet endedness bug

    @rroutsong
    rroutsong committed Feb 6, 2024
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  2. fix: rework resources for demuxing and qc of certain rules

    @rroutsong
    rroutsong committed Feb 6, 2024
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  3. fix: correct overindentation

    @rroutsong
    rroutsong committed Feb 6, 2024
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  4. fix: correct bugs with lscratch usage for fastqc rule

    @rroutsong
    rroutsong committed Feb 6, 2024
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Commits on Feb 7, 2024

  1. fix: formatting

    @rroutsong
    rroutsong committed Feb 7, 2024
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  2. fix: update biowulf scheduler interactions for lscratch

    @rroutsong
    rroutsong committed Feb 7, 2024
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  3. feat: switch to main branch on submodule

    @rroutsong
    rroutsong committed Feb 7, 2024
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Commits on Feb 8, 2024

  1. fix: update dry-run snakemake args and refactor tmpdir handling in fa… 

    …stqc rule
    @rroutsong
    rroutsong committed Feb 8, 2024
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  2. fix: ignore test dry run output

    @rroutsong
    rroutsong committed Feb 8, 2024
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  3. fix: correct git ignore path

    @rroutsong
    rroutsong committed Feb 8, 2024
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  4. fix: recursive gitignore

    @rroutsong
    rroutsong committed Feb 8, 2024
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  5. fix: correct github action issues with escape and snakemake args

    @rroutsong
    rroutsong committed Feb 8, 2024
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  6. fix: remove -r from snakemake

    @rroutsong
    rroutsong committed Feb 8, 2024
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  7. fix: remove profile designation from dry run execution

    @rroutsong
    rroutsong committed Feb 8, 2024
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  8. fix: run ci on snakemake 7.32.4 in parallel to stable version

    @rroutsong
    rroutsong committed Feb 8, 2024
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  9. fix: addresssing incompatibility with snakemake>=8.0.0

    @rroutsong
    rroutsong committed Feb 8, 2024
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