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Dev > Master, v1.0 release #61

Merged
merged 44 commits into from
Aug 20, 2018
Merged

Dev > Master, v1.0 release #61

merged 44 commits into from
Aug 20, 2018

Commits on Aug 9, 2018

  1. First efforts to generate bigWig files

    Alexander Peltzer committed Aug 9, 2018
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  2. Add deeptools as dependency

    Alexander Peltzer committed Aug 9, 2018
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  3. Fix subsampling steps in RNAseq

    Alexander Peltzer committed Aug 9, 2018
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  4. Add createBigWig to base.config

    Alexander Peltzer committed Aug 9, 2018
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  5. Probably missing collect

    Alexander Peltzer committed Aug 9, 2018
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  6. Fix suffix

    Alexander Peltzer committed Aug 9, 2018
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Commits on Aug 10, 2018

  1. Merge branch 'master' into master

    @apeltzer
    apeltzer authored Aug 10, 2018
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  2. Fix rnaseq pipeline crashes with large input files; Add sequencing ce… 

    …nter in BAM
    @jun-wan
    jun-wan committed Aug 10, 2018
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  3. Back to old Dockerfile syntax

    Alexander Peltzer committed Aug 10, 2018
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  4. Removed bigwig from basename - its not bam anymore

    Alexander Peltzer committed Aug 10, 2018
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  5. Merge branch 'master' of https://github.com/apeltzer/RNAseq

    Alexander Peltzer committed Aug 10, 2018
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  6. Merge branch 'master' into master

    @apeltzer
    apeltzer authored Aug 10, 2018
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  7. Little update for environment

    Alexander Peltzer committed Aug 10, 2018
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  8. Just remove sorted suffix

    Alexander Peltzer committed Aug 10, 2018
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  9. Remove entire suffix

    Alexander Peltzer committed Aug 10, 2018
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Commits on Aug 11, 2018

  1. Fixing baseName usage

    Alexander Peltzer committed Aug 11, 2018
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  2. Don't remove sorted

    Alexander Peltzer committed Aug 11, 2018
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  3. Theres no bam

    Alexander Peltzer committed Aug 11, 2018
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  4. remove collect

    Alexander Peltzer committed Aug 11, 2018
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  5. Add travis_wait / hopefully no more timeouts

    Alexander Peltzer committed Aug 11, 2018
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  6. Moving the log not required anymore

    Alexander Peltzer committed Aug 11, 2018
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  7. Still need a txt extension though

    Alexander Peltzer committed Aug 11, 2018
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Commits on Aug 12, 2018

  1. Remove travis wait

    Alexander Peltzer committed Aug 12, 2018
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Commits on Aug 13, 2018

  1. update default seeting in base.config and minor changes in main.nf

    @jun-wan
    jun-wan committed Aug 13, 2018
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  2. update default seeting in base.config and minor changes in main.nf

    @jun-wan
    jun-wan committed Aug 13, 2018
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  3. Merge pull request #53 from apeltzer/master 

    BigWig support instead of subsample
    @ewels
    ewels authored Aug 13, 2018
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Commits on Aug 14, 2018

  1. Fix syntax error from the Travis CI test

    @jun-wan
    jun-wan committed Aug 14, 2018
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Commits on Aug 16, 2018

  1. Merge pull request #56 from jun-wan/master 

    Pipeline crashes with large input files; Add sequencing center in BAM
    @ewels
    ewels authored Aug 16, 2018
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  2. Pull upstream and fix conflicts

    @ewels
    ewels committed Aug 16, 2018
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  3. Get the linting tests to pass

    @ewels
    ewels committed Aug 16, 2018
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  4. Update STAR version to latest (fixing segfaults)

    Alexander Peltzer committed Aug 16, 2018
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  5. Switch from old nextflow & pipeline param usage to new manifest.

    @ewels
    ewels committed Aug 16, 2018
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  6. Merge pull request #59 from apeltzer/master 

    Update STAR version to latest (fixing segfaults)
    @ewels
    ewels authored Aug 16, 2018
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Commits on Aug 17, 2018

  1. Fix containsKey if no genome is used

    Alexander Peltzer committed Aug 17, 2018
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  2. Merge pull request #60 from apeltzer/master 

    Fix containsKey if no genome is used
    @ewels
    ewels authored Aug 17, 2018
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  3. Remove manifest.pipelineVersion from main.nf 

    Hopefully we can go back to only using this in a future version of nextflow.
    @ewels
    ewels committed Aug 17, 2018
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Commits on Aug 18, 2018

  1. Merge pull request #58 from ewels/master 

    Getting the lint tests to pass
    @sven1103
    sven1103 authored Aug 18, 2018
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Commits on Aug 20, 2018

  1. Bump version number to v1.0 and write changelog

    @ewels
    ewels committed Aug 20, 2018
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  2. Changelog typo fixed

    @ewels
    ewels committed Aug 20, 2018
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  3. Merge pull request #62 from ewels/master 

    Bump version number to v1.0 and write changelog
    @sven1103
    sven1103 authored Aug 20, 2018
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  4. Remove cheeky backslashes that crept in after version bump

    @ewels
    ewels committed Aug 20, 2018
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  5. Merge pull request #63 from ewels/master 

    Remove cheeky backslashes that crept in after version bump
    @apeltzer
    apeltzer authored Aug 20, 2018
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  6. Add missing deepTools output for MultiQC/Report

    Alexander Peltzer committed Aug 20, 2018
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  7. Merge pull request #64 from apeltzer/master 

    MultiQC Report for deepTools
    @ewels
    ewels authored Aug 20, 2018
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