Code

Assembly/Binning#5

Code

Merged

HadrienG merged 56 commits intomasternf-core/mag:masterfrom devnf-core/mag:devCopy head branch name to clipboardJan 21, 2019

Commits

Commits on Oct 1, 2018

• fix version

  HadrienG

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Commits on Oct 3, 2018

• make travis happy before building the actual pipeline

  HadrienG

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Commits on Oct 5, 2018

• add logo

  maxulysse

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• Merge pull request #6 from MaxUlysse/master

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  ewels

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• Update README.md

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  maxulysse

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• Merge pull request #7 from nf-core/MaxUlysse-patch-1

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Commits on Oct 9, 2018

• assembly

  HadrienG

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• Merge branch 'dev' of https://github.com/nf-core/mag into dev

  HadrienG

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• bump nextflow version

  HadrienG

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Commits on Oct 10, 2018

• binning

  HadrienG

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• switch to profile for tests

  HadrienG

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Commits on Oct 25, 2018

• checkm

  HadrienG

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Commits on Oct 29, 2018

• smaller test data

  HadrienG

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• working minimal test file producing bins

  HadrienG

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Commits on Oct 30, 2018

• tool update

  HadrienG

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• added fastqc

  HadrienG

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• added quast

  HadrienG

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• checkm plots

  HadrienG

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Commits on Nov 16, 2018

• added checkm refine fastp

  HadrienG

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• atropos -> fastp

  HadrienG

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• check automatic bin merghing

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Commits on Nov 19, 2018

• into -> from

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• no need for subdir

  HadrienG

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  16f1e73

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• fix bin input

  HadrienG

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• debug checkm

  HadrienG

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Commits on Nov 20, 2018

• do not need custome checkm docker anymore

  HadrienG

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• refinem

  HadrienG

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• task cpus

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Commits on Nov 23, 2018

• one-liner works without head (no more SIGPIPE)

  HadrienG

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  cc7f2c9

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• beter bash quoting + adapter params

  HadrienG

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• more software versions

  HadrienG

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  72c7a19

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• more fastp options

  HadrienG

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• single end support

  HadrienG

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Commits on Nov 26, 2018

• checkm and metabat options

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  b35dad2

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Commits on Dec 5, 2018

• refinem

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Commits on Dec 6, 2018

• refinem filter ssu evalue threshold

  HadrienG

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  32670c8

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• docs and output names

  HadrienG

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  fd4f2ea

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• version bump (0.1.0dev -> 0.1.0)

  HadrienG

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• only dev exists on docker hub

  HadrienG

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Commits on Dec 13, 2018

• version number -> 1.0.0

  HadrienG

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• tag to 1.0.0

  HadrienG

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• singularity to 1.0.0

  HadrienG

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Commits on Jan 5, 2019

• submitted missing packages in bioconda

  HadrienG

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• no pip install

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Commits on Jan 7, 2019

• test config

  HadrienG

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• move checkm db download to main.nf

  HadrienG

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• MAINTAINER is deprecated

  HadrienG

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Commits on Jan 14, 2019

• minor docs improvements

  HadrienG

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  4e38a5c

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• allow loading of custom configs

  HadrienG

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  1ea62a7

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• fix checkm db

  HadrienG

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Commits on Jan 15, 2019

• remove singularity hub

  HadrienG

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• move time to base.config

  HadrienG

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• remove some old comments

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Commits on Jan 17, 2019

• software versions

  HadrienG

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Commits on Jan 18, 2019

• rename fastqc config

  HadrienG

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• manifest + moved multiples into into processes

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