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Add multiqc #14

Merged
merged 33 commits into from
Oct 31, 2023
Merged

Add multiqc #14

merged 33 commits into from
Oct 31, 2023

Commits on Oct 5, 2023

  1. add ngs_qa_qc dockerfile and ep

    @rroutsong
    rroutsong committed Oct 5, 2023
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  2. begin restructuring of workflows for extension of demux workflow

    @rroutsong
    rroutsong committed Oct 5, 2023
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Commits on Oct 6, 2023

  1. merge in dry_run action changes

    @rroutsong
    rroutsong committed Oct 6, 2023
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  2. start ngs qc/qa pipeline, fastqc - trimmed/untrimmed + fastp trimming

    @rroutsong
    rroutsong committed Oct 6, 2023
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Commits on Oct 10, 2023

  1. ngsqc fastqc, trimming, fastqc again after trim

    @rroutsong
    rroutsong committed Oct 10, 2023
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Commits on Oct 11, 2023

  1. fix line endings on ep.sh

    @rroutsong
    rroutsong committed Oct 11, 2023
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  2. add in fastq screen config to docker

    @rroutsong
    rroutsong committed Oct 11, 2023
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Commits on Oct 12, 2023

  1. final ngsqc dockerfile

    @rroutsong
    rroutsong committed Oct 12, 2023
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Commits on Oct 13, 2023

  1. feat: expand ngs qc workflow

    @rroutsong
    rroutsong committed Oct 13, 2023
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  2. feat: python module support for ngs qc-qa

    @rroutsong
    rroutsong committed Oct 13, 2023
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  3. chore: ignore jsons, lower latentcy wait for biowulf

    @rroutsong
    rroutsong committed Oct 13, 2023
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Commits on Oct 17, 2023

  1. feat: finalize first half of ngsqc pipeline

    @rroutsong
    rroutsong committed Oct 17, 2023
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  2. fix: snakemake pathing correction

    @rroutsong
    rroutsong committed Oct 17, 2023
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  3. fix: dry run action needs -s kwarg

    @rroutsong
    rroutsong committed Oct 17, 2023
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  4. chore: fix args in github action

    @rroutsong
    rroutsong committed Oct 17, 2023
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  5. chore: refactor setuptools package, force include workflow and profil… 

    …es, fix dry run command
    @rroutsong
    rroutsong committed Oct 17, 2023
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  6. chore: dry run command not being executed

    @rroutsong
    rroutsong committed Oct 17, 2023
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Commits on Oct 19, 2023

  1. feat: kaiju and kraken annotation rules, beginning

    @rroutsong
    rroutsong committed Oct 19, 2023
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  2. chore: merge in conda2src changes, drop using conda

    @rroutsong
    rroutsong committed Oct 19, 2023
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  3. chore: fix more merge conflicts

    @rroutsong
    rroutsong committed Oct 19, 2023
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Commits on Oct 24, 2023

  1. feat: working kraken & kaiju

    @rroutsong
    rroutsong committed Oct 24, 2023
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  2. chore: remap outputs to discussed structure

    @rroutsong
    rroutsong committed Oct 24, 2023
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  3. fix: align io paths for ngsqc workflow

    @rroutsong
    rroutsong committed Oct 24, 2023
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Commits on Oct 25, 2023

  1. chore: relocate slurm logs directory

    @rroutsong
    rroutsong committed Oct 25, 2023
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  2. fix: correct fastqc_trimmed output paths

    @rroutsong
    rroutsong committed Oct 25, 2023
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  3. fix: dry run action, add path to env

    @rroutsong
    rroutsong committed Oct 25, 2023
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  4. fix: broken path in dry run action

    @rroutsong
    rroutsong committed Oct 25, 2023
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  5. fix: cat from /Users/routsongrm/git/NGS/Dmux

    @rroutsong
    rroutsong committed Oct 25, 2023
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  6. fix: cat from \$PWD/NGS/Dmux

    @rroutsong
    rroutsong committed Oct 25, 2023
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  7. Merge remote-tracking branch 'refs/remotes/origin/add_kaiju_kraken' i… 

    …nto add_kaiju_kraken
    @rroutsong
    rroutsong committed Oct 25, 2023
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  8. feat: add multiqc report

    @rroutsong
    rroutsong committed Oct 25, 2023
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  9. chore: merge in main, fix mutliqc output report name

    @rroutsong
    rroutsong committed Oct 25, 2023
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  10. fix: new flag for dry run in CI

    @rroutsong
    rroutsong committed Oct 25, 2023
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