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Redux #13

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Redux #13

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Commits on Sep 21, 2023

  1. Merge pull request #4 from Tony-xy-Liu/fix_endmapping 

    check implementation
    @Tony-xy-Liu
    Tony-xy-Liu authored Sep 21, 2023
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  2. Merge pull request #5 from Tony-xy-Liu/dev 

    update master
    @Tony-xy-Liu
    Tony-xy-Liu authored Sep 21, 2023
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Commits on Oct 4, 2023

  1. Merge pull request #6 from hallamlab/master 

    Conda channel name change
    @Tony-xy-Liu
    Tony-xy-Liu authored Oct 4, 2023
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  2. Merge pull request #7 from Tony-xy-Liu/master 

    Conda channel name change
    @Tony-xy-Liu
    Tony-xy-Liu authored Oct 4, 2023
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Commits on Nov 6, 2023

  1. rename old

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 6, 2023
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Commits on Nov 11, 2023

  1. move old files

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 11, 2023
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  2. redux up to assembly

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 11, 2023
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Commits on Nov 12, 2023

  1. pre delete constants.py

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 12, 2023
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Commits on Nov 15, 2023

  1. rename step

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 15, 2023
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  2. pre contig selector

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. pre remove mafft

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 16, 2023
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  2. end mapping

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 16, 2023
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Commits on Nov 21, 2023

  1. failed contig selection

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 21, 2023
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  2. update docker

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 21, 2023
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  3. more docker fixes + samtools to env

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 21, 2023
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Commits on Nov 23, 2023

  1. working end mapping, unverified

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 23, 2023
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  2. better contig selection + minor improvements

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 23, 2023
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  3. tweaks to contig selection output

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 23, 2023
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  4. rename step to scaffold

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 23, 2023
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  5. rename step to scaffold

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 23, 2023
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  6. enable using previous assemblies

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 23, 2023
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Commits on Nov 24, 2023

  1. enable bypassing steps + end mapping

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 24, 2023
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  2. assembly coverage and stats

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 24, 2023
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  3. fastqc

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 24, 2023
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  4. cleanup

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 24, 2023
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  5. delete verison 1

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 24, 2023
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Commits on Nov 27, 2023

  1. prep annot and size est

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 27, 2023
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  2. remove blast ver req in favour of dependencies

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. pool size estimate

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 28, 2023
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  2. metapathways

    @Tony-xy-Liu
    Tony-xy-Liu committed Nov 28, 2023
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Commits on Dec 2, 2023

  1. metapathways standardized gffs

    @Tony-xy-Liu
    Tony-xy-Liu committed Dec 2, 2023
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Commits on Dec 7, 2023

  1. upgrade snakemake shell from os.system

    @Tony-xy-Liu
    Tony-xy-Liu committed Dec 7, 2023
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Commits on Feb 5, 2024

  1. test suite

    @Tony-xy-Liu
    Tony-xy-Liu committed Feb 5, 2024
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Commits on Mar 15, 2024

  1. move

    @Tony-xy-Liu
    Tony-xy-Liu committed Mar 15, 2024
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Commits on Mar 28, 2024

  1. pre manuscript d1

    @Tony-xy-Liu
    Tony-xy-Liu committed Mar 28, 2024
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Commits on Jun 21, 2024

  1. min contig length as param

    @Tony-xy-Liu
    Tony-xy-Liu committed Jun 21, 2024
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  2. correct entrypoint after mambabuild update

    @Tony-xy-Liu
    Tony-xy-Liu committed Jun 21, 2024
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