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Version 1.1 merge Master > Dev#140

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sven1103 merged 117 commits intomasternf-core/tools:masterfrom devnf-core/tools:devCopy head branch name to clipboardAug 14, 2018

+2,308-110

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Commits on Jul 17, 2018

• Refactor dependency management

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Commits on Jul 18, 2018

• Merge pull request #76 from sven1103/patch-1/fix-broken-pip-installation

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Commits on Aug 6, 2018

• fix CI with new MultiQC version in minimal example

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• Merge pull request #82 from MaxUlysse/master

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Commits on Aug 7, 2018

• Moved cookiecutter template into tools repo.

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• Simplified template variables.

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Commits on Aug 8, 2018

• Merge branch 'dev' of github.com:nf-core/tools

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• Fix merge conflict

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• Provide helper script for template changes

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• Added git init to cookiecutter

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• Perform some small refactoring

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• Merge pull request #89 from nf-core/master

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• Don't use reserved name init

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• Remove redundant config linesW

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• Changelog update

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• Merge pull request #83 from ewels/cookiecutter_merge

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• add templates for community requirements cf #87

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• add nf-core to cookiecutter.pipeline_slug + some typos

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• forgot some nf-core ...

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• improve PR template

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• add withName syntax, fixes #100

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• Use new manifest.nextflowVersion instead of params.minNextflowVersion

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• Updated with recent cookiecutter updates

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• Travis: Make new pipeline and run lint tests

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• Merge pull request #107 from ewels/template_update

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• Readme: Add docs about nf-core create

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• Applied changes from @apeltzer in nf-core/cookiecutter#57 (#109)

  

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Commits on Aug 9, 2018

• more line-breaks and update docs

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• Add check to lint for deprecated syntax (#104)

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• Merge branch 'dev' into withName_syntax

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• Merge pull request #105 from jemten/withName_syntax

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• lint fails more gracefully in travis dont have before_install

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• Added manifest.name and manifest.pipelineVersion

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• Added a few more line breaks

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• Merge pull request #90 from MaxUlysse/dev

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• Merged upstream changes

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• Merge branch 'master' into test-cookiecutter

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• Merge upstream changes

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• Merge pull request #110 from ewels/update-readme-create

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• Added nfcore- prefix to conda env name in template

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• Update release, add nf-core prefix to template.

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• Make lint error command more user friendly

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• Travis: Don't pull a docker image tag

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• Docs and lint test example

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• Merge pull request #106 from ewels/nextflowVersion

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• Refactor a lot of stuff

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• Remove last warning for template update

  

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• Merge remote-tracking branch 'upstream/dev'

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• Get rid of last pipeline linting warning by using newest MQC

  

  Alexander Peltzer

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• Merge remote-tracking branch 'upstream/dev'

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• Merge pull request #108 from ewels/test-cookiecutter

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• Overwrite template content from new version

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• Merge pull request #118 from nf-core/updateTemplate

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• Assert for travis tag and add comments

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• Add workflow summary to MultiQC

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• Provide Travis Tag in PR

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• Fix broken markdown syntax

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• Add workflow summary to MultiQC

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• solving conflicts

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• Merge branch 'dev' into release-updateTravis

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• Merge pull request #116 from ewels/release-updateTravis

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• Use bot token for authenticated services

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

  

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• Probably a line feed error

  

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• Merge upstream changes. Fake docker tag on travis config.

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• Merge pull request #121 from nf-core/fix-vis-error

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• Tidy up

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• cookiecutter.pipeline_name -> cookiecutter.pipeline_slug

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• Upate linting and tests for new travis docker tag hack

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• merged with upstream

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• reverse conda env handling (fix for #114)

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• Updated template to tag docker as latest in travis

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• Deleted now removed nextflow version check warning

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• Minor tweaks

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• Merge pull request #120 from jemten/create_workflow_summary

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Commits on Aug 10, 2018

• update test files

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• more tests are expected to fail (due to ENV line)

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• Merge pull request #117 from ewels/travis_dockerpull

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• Fix merge conflict

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• Merge branch 'HadrienG-conda' into dev

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• Merge branch 'dev' into moreManifest

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• Fix number of expected passing tests

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• Update template files to use reverted conda ENV hack

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• Use .startswith() as it's nicer

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• Added back the quote mark stripping

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• Merge pull request #115 from ewels/moreManifest

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Commits on Aug 12, 2018

• Phil's attempt at failing master merges

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Commits on Aug 13, 2018

• Merge pull request #132 from ewels/travisFailMaster

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• Updated the documentation for cookiecutter (#123)

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• Refactor sync tools

  sven1103

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• Introduce better expection handling

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Commits on Aug 14, 2018

• Fixed config bug in singularity profile

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• Docs redundancy (#124)

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• Merge pull request #134 from nf-core/singularity-profile-bugfix

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• Quote the new .travis.yaml tests

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• Update repo template travis config

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• Fix docs templating errors

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• Merge pull request #135 from nf-core/travis-fix

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• Use cookiecutter function from nf_core

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• nf-core create: Refactor, add --outdir

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• Merge pull request #136 from ewels/master

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• Merge remote-tracking branch 'origin' into dev

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• Update pipeline creation code

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• Refactor sync

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• Make --force work for nf-core create

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• Merge pull request #138 from ewels/master

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• Let the create command move the template

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• Merge pull request #137 from sven1103/dev

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• Refactored cookiecutter variables, overhauled docs

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• Noticed the changelog was waaay out of date

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• Fixed linting dirname error and conda env name lint failure

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• Fix the tests with hyphens in new places

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• Merge pull request #139 from ewels/master

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• v1.1 version bump & changelog update

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• Merge pull request #141 from ewels/master

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• Use config.get to avoid KeyErrors. Don't use --release for nf-core/tools

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• Merge pull request #142 from ewels/master

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