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Refactor codebase #41

Merged
merged 30 commits into from
Aug 7, 2024
Merged

Refactor codebase #41

merged 30 commits into from
Aug 7, 2024

Commits on Jun 27, 2024

  1. chore: refactor rule all, move some files to more appropriate locations

    @rroutsong
    rroutsong committed Jun 27, 2024
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Commits on Jul 5, 2024

  1. chore: refactor script locations, workflow rules, remove uropa rules … 

    …for time being
    @rroutsong
    rroutsong committed Jul 5, 2024
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Commits on Jul 8, 2024

  1. fix: correct diffbindedger output paths

    @rroutsong
    rroutsong committed Jul 8, 2024
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  2. chore: add back bin scripts, correct pathing for bin scripts, formatting

    @rroutsong
    rroutsong committed Jul 8, 2024
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Commits on Jul 10, 2024

  1. fix: remove old imports, duplicate parameters

    @rroutsong
    rroutsong committed Jul 10, 2024
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  2. fix: correct typo type to _type

    @rroutsong
    rroutsong committed Jul 10, 2024
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  3. fix: correct pathing on diffbind outputs

    @rroutsong
    rroutsong committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. fix: missing imports in peakcall rules

    @rroutsong
    rroutsong committed Jul 11, 2024
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  2. fix: indent

    @rroutsong
    rroutsong committed Jul 11, 2024
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  3. fix: fix single end functionality in bwa rule

    @rroutsong
    rroutsong committed Jul 11, 2024
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  4. chore: spacing, refactor manorm rule

    @rroutsong
    rroutsong committed Jul 11, 2024
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  5. fix: reference global tmpdir and paired_end flag

    @rroutsong
    rroutsong committed Jul 11, 2024
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  6. fix: fix rep switch

    @rroutsong
    rroutsong committed Jul 11, 2024
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  7. chore: more spacing, fix reps flag reversal

    @rroutsong
    rroutsong committed Jul 11, 2024
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Commits on Jul 15, 2024

  1. chore: make bin files executable, fix execution issues from test data… 

    … runs
    @rroutsong
    rroutsong committed Jul 15, 2024
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Commits on Jul 22, 2024

  1. fix: working out bugs discovered on AV

    @rroutsong
    rroutsong committed Jul 22, 2024
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Commits on Jul 29, 2024

  1. fix: testing corrections

    @rroutsong
    rroutsong committed Jul 29, 2024
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Commits on Jul 31, 2024

  1. fix: comment out manorm rules for now

    @rroutsong
    rroutsong committed Jul 31, 2024
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  2. fix: turn off sicer involved inputs in cfchip pipeline

    @rroutsong
    rroutsong committed Jul 31, 2024
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  3. fix: realign uropa, promotertable2, diffbind outputs inputs

    @rroutsong
    rroutsong committed Jul 31, 2024
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  4. fix: realign promotertable cfchip inputs

    @rroutsong
    rroutsong committed Jul 31, 2024
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Commits on Aug 2, 2024

  1. Delete workflow/chrom-seek.code-workspace

    @skchronicles
    skchronicles authored Aug 2, 2024
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  2. fix: minor review fixes, reverting some dev settings

    @rroutsong
    rroutsong committed Aug 2, 2024
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  3. Merge branch 'refactor_codebase' of http://github.com/OpenOmics/chrom… 

    …-seek into refactor_codebase
    @rroutsong
    rroutsong committed Aug 2, 2024
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  4. fix: comment out debug-dag from dryrun snakemake execution

    @rroutsong
    rroutsong committed Aug 2, 2024
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Commits on Aug 6, 2024

  1. fix: reconfigure a few outputs based on test runs

    @rroutsong
    rroutsong committed Aug 6, 2024
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  2. fix: refactor diffbind prep script, add error case exception for umap… 

    … in diffbindqc rmd
    @rroutsong
    rroutsong committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Update prep_diffbind.py 

    Adding ending carriage return to output files
    @tovahmarkowitz
    tovahmarkowitz authored Aug 7, 2024
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  2. fix: add blocking/control functions to grouping header

    @rroutsong
    rroutsong committed Aug 7, 2024
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  3. Merge branch 'refactor_codebase' of http://github.com/OpenOmics/chrom… 

    …-seek into refactor_codebase
    @rroutsong
    rroutsong committed Aug 7, 2024
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