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Merge v0.7.0 to main #111

Merged
merged 43 commits into from
Aug 11, 2023
Merged

Merge v0.7.0 to main #111

merged 43 commits into from
Aug 11, 2023

Commits on Jul 26, 2023

  1. Merge pull request #102 from rhysnewell/main 

    Catch dev up to main
    @rhysnewell
    rhysnewell authored Jul 26, 2023
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Commits on Jul 27, 2023

  1. add test for recover_mags_no_singlem workflow

    @AroneyS
    AroneyS committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. add refinery max iterations argument

    @AroneyS
    AroneyS committed Jul 28, 2023
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  2. add test runner on pull_request

    @AroneyS
    AroneyS committed Jul 28, 2023
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  3. add bin check to checkm_metabat2 and checkm_semibin

    @AroneyS
    AroneyS committed Jul 28, 2023
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  4. skip checkm_{binner} rules when refinery iterations 0

    @AroneyS
    AroneyS committed Jul 28, 2023
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  5. add note about iterations=0

    @AroneyS
    AroneyS committed Jul 28, 2023
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  6. set max iterations type to int

    @AroneyS
    AroneyS committed Jul 28, 2023
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  7. add more friendly message when skipping refinery

    @AroneyS
    AroneyS committed Jul 28, 2023
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  8. Merge pull request #103 from AroneyS/add-refinery-max-iterations-arg 

    Add refinery max iterations arg
    @AroneyS
    AroneyS authored Jul 28, 2023
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Commits on Jul 31, 2023

  1. add refinery_max_iterations to checkm rules

    @AroneyS
    AroneyS committed Jul 31, 2023
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  2. update to semibin2

    @AroneyS
    AroneyS committed Jul 31, 2023
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  3. ensure bins are copied when refinement is skipped

    @AroneyS
    AroneyS committed Jul 31, 2023
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  4. rework skip binners test

    @AroneyS
    AroneyS committed Jul 31, 2023
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  5. fix short recovery only test

    @AroneyS
    AroneyS committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. Merge pull request #104 from rhysnewell/update-to-semibin2 

    Update to semibin2
    @rhysnewell
    rhysnewell authored Aug 1, 2023
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  2. fix checkm subprocess

    @AroneyS
    AroneyS committed Aug 1, 2023
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  3. fix test

    @AroneyS
    AroneyS committed Aug 1, 2023
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  4. revert shell=True and fix subprocess call

    @AroneyS
    AroneyS committed Aug 1, 2023
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  5. Merge pull request #105 from rhysnewell/fix-checkm-subprocess 

    Fix checkm subprocess
    @rhysnewell
    rhysnewell authored Aug 1, 2023
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Commits on Aug 3, 2023

  1. fix: removal of instances of shell=True

    rhysnewell committed Aug 3, 2023
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  2. put shell=True back into main process command to debug

    rhysnewell committed Aug 3, 2023
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  3. put shell=True back into main process command to debug

    rhysnewell committed Aug 3, 2023
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  4. convert to run with no shell=True

    rhysnewell committed Aug 3, 2023
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  5. convert to run with no shell=True

    rhysnewell committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. fix: initial subprocess command, removed quotes around config.yaml path

    rhysnewell committed Aug 4, 2023
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  2. update complex piped subprocess commands, needs testing

    rhysnewell committed Aug 4, 2023
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Commits on Aug 5, 2023

  1. replace commands in polish.py, needs testing

    rhysnewell committed Aug 5, 2023
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  2. all relevant instances of shell=True converted

    rhysnewell committed Aug 5, 2023
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Commits on Aug 8, 2023

  1. fix #108 update concoct recipe to limit sklean version

    rhysnewell committed Aug 8, 2023
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  2. fix: set TMPDIR env var before subprocess call. remove hardcoded cond… 

    …a paths in tests
    rhysnewell committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. fix: tests and graceful exits on singlem. Move finalise stats

    rhysnewell committed Aug 9, 2023
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  2. revert: add conda-prefix to test commands

    rhysnewell committed Aug 9, 2023
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  3. fix: typo finalize -> finalise

    rhysnewell committed Aug 9, 2023
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  4. add long-read integration test 

    long reads simulated with pbsim2 R95.model 23:31:46
filtered first 20 reads from each file and deduplicated
    @AroneyS
    AroneyS committed Aug 9, 2023
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  5. cleanup pdb call

    @AroneyS
    AroneyS committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. fix: polish.py and pipeing commands

    @rhysnewell
    rhysnewell committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. fix: add bam index creation in map_reads_ref rule

    @rhysnewell
    rhysnewell committed Aug 11, 2023
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  2. assembly not expected since it is input

    @AroneyS
    AroneyS committed Aug 11, 2023
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  3. fix: singlem script no longer uses glob

    @rhysnewell
    rhysnewell committed Aug 11, 2023
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  4. Merge pull request #107 from rhysnewell/sanitise_subprocess_calls 

    fix: removal of instances of shell=True
    @rhysnewell
    rhysnewell authored Aug 11, 2023
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  5. update: v0.7.0

    @rhysnewell
    rhysnewell committed Aug 11, 2023
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  6. Merge pull request #110 from rhysnewell/v0.7.0 

    update: v0.7.0
    @rhysnewell
    rhysnewell authored Aug 11, 2023
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