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Assembly/Binning #5

Merged
merged 56 commits into from
Jan 21, 2019
Merged

Assembly/Binning #5

merged 56 commits into from
Jan 21, 2019

Commits on Oct 1, 2018

  1. fix version

    @HadrienG
    HadrienG committed Oct 1, 2018
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Commits on Oct 3, 2018

  1. make travis happy before building the actual pipeline

    @HadrienG
    HadrienG committed Oct 3, 2018
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Commits on Oct 5, 2018

  1. add logo

    @maxulysse
    maxulysse committed Oct 5, 2018
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  2. Merge pull request #6 from MaxUlysse/master 

    add logo
    @ewels
    ewels authored Oct 5, 2018
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  3. Update README.md 

    fix double .png
    @maxulysse
    maxulysse authored Oct 5, 2018
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  4. Merge pull request #7 from nf-core/MaxUlysse-patch-1 

    Update README.md
    @ewels
    ewels authored Oct 5, 2018
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Commits on Oct 9, 2018

  1. assembly

    @HadrienG
    HadrienG committed Oct 9, 2018
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  2. Merge branch 'dev' of https://github.com/nf-core/mag into dev

    @HadrienG
    HadrienG committed Oct 9, 2018
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  3. bump nextflow version

    @HadrienG
    HadrienG committed Oct 9, 2018
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Commits on Oct 10, 2018

  1. binning

    @HadrienG
    HadrienG committed Oct 10, 2018
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  2. switch to profile for tests

    @HadrienG
    HadrienG committed Oct 10, 2018
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Commits on Oct 25, 2018

  1. checkm

    @HadrienG
    HadrienG committed Oct 25, 2018
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Commits on Oct 29, 2018

  1. smaller test data

    @HadrienG
    HadrienG committed Oct 29, 2018
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  2. working minimal test file producing bins

    @HadrienG
    HadrienG committed Oct 29, 2018
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Commits on Oct 30, 2018

  1. tool update

    @HadrienG
    HadrienG committed Oct 30, 2018
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  2. added fastqc

    @HadrienG
    HadrienG committed Oct 30, 2018
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  3. added quast

    @HadrienG
    HadrienG committed Oct 30, 2018
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  4. checkm plots

    @HadrienG
    HadrienG committed Oct 30, 2018
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Commits on Nov 16, 2018

  1. added checkm refine fastp

    @HadrienG
    HadrienG committed Nov 16, 2018
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  2. atropos -> fastp

    @HadrienG
    HadrienG committed Nov 16, 2018
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  3. check automatic bin merghing

    @HadrienG
    HadrienG committed Nov 16, 2018
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Commits on Nov 19, 2018

  1. into -> from

    @HadrienG
    HadrienG committed Nov 19, 2018
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  2. no need for subdir

    @HadrienG
    HadrienG committed Nov 19, 2018
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  3. fix bin input

    @HadrienG
    HadrienG committed Nov 19, 2018
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  4. debug checkm

    @HadrienG
    HadrienG committed Nov 19, 2018
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Commits on Nov 20, 2018

  1. do not need custome checkm docker anymore

    @HadrienG
    HadrienG committed Nov 20, 2018
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  2. refinem

    @HadrienG
    HadrienG committed Nov 20, 2018
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  3. task cpus

    @HadrienG
    HadrienG committed Nov 20, 2018
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Commits on Nov 23, 2018

  1. one-liner works without head (no more SIGPIPE)

    @HadrienG
    HadrienG committed Nov 23, 2018
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  2. beter bash quoting + adapter params

    @HadrienG
    HadrienG committed Nov 23, 2018
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  3. more software versions

    @HadrienG
    HadrienG committed Nov 23, 2018
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  4. more fastp options

    @HadrienG
    HadrienG committed Nov 23, 2018
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  5. single end support

    @HadrienG
    HadrienG committed Nov 23, 2018
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Commits on Nov 26, 2018

  1. checkm and metabat options

    @HadrienG
    HadrienG committed Nov 26, 2018
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Commits on Dec 5, 2018

  1. refinem

    @HadrienG
    HadrienG committed Dec 5, 2018
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Commits on Dec 6, 2018

  1. refinem filter ssu evalue threshold

    @HadrienG
    HadrienG committed Dec 6, 2018
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  2. docs and output names

    @HadrienG
    HadrienG committed Dec 6, 2018
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  3. version bump (0.1.0dev -> 0.1.0)

    @HadrienG
    HadrienG committed Dec 6, 2018
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  4. only dev exists on docker hub

    @HadrienG
    HadrienG committed Dec 6, 2018
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Commits on Dec 13, 2018

  1. version number -> 1.0.0

    @HadrienG
    HadrienG committed Dec 13, 2018
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  2. tag to 1.0.0

    @HadrienG
    HadrienG committed Dec 13, 2018
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  3. singularity to 1.0.0

    @HadrienG
    HadrienG committed Dec 13, 2018
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Commits on Jan 5, 2019

  1. submitted missing packages in bioconda

    @HadrienG
    HadrienG committed Jan 5, 2019
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  2. no pip install

    @HadrienG
    HadrienG committed Jan 5, 2019
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Commits on Jan 7, 2019

  1. test config

    @HadrienG
    HadrienG committed Jan 7, 2019
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  2. move checkm db download to main.nf

    @HadrienG
    HadrienG committed Jan 7, 2019
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  3. MAINTAINER is deprecated

    @HadrienG
    HadrienG committed Jan 7, 2019
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Commits on Jan 14, 2019

  1. minor docs improvements

    @HadrienG
    HadrienG committed Jan 14, 2019
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  2. allow loading of custom configs

    @HadrienG
    HadrienG committed Jan 14, 2019
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  3. fix checkm db

    @HadrienG
    HadrienG committed Jan 14, 2019
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Commits on Jan 15, 2019

  1. remove singularity hub

    @HadrienG
    HadrienG committed Jan 15, 2019
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  2. move time to base.config

    @HadrienG
    HadrienG committed Jan 15, 2019
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  3. remove some old comments

    @HadrienG
    HadrienG committed Jan 15, 2019
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Commits on Jan 17, 2019

  1. software versions

    @HadrienG
    HadrienG committed Jan 17, 2019
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Commits on Jan 18, 2019

  1. rename fastqc config

    @HadrienG
    HadrienG committed Jan 18, 2019
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  2. manifest + moved multiples into into processes

    @HadrienG
    HadrienG committed Jan 18, 2019
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