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Pseudo-PR: First release review! #45

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matq007 wants to merge 200 commits intopseudo-prnf-core/rnafusion:pseudo-prfrom masternf-core/rnafusion:masterCopy head branch name to clipboard

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Commits

Commits on May 29, 2017

• Starte don some conifg options

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Commits on Jun 13, 2017

• Added STAR-fusion process

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Commits on Jun 14, 2017

• added FusionInspector process

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Commits on Aug 22, 2017

• Started on the fusionCatcher process

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• bugfixing FusionCatcher process

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• Merge pull request #1 from Hammarn/master

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• Untested code tidying.

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Commits on Aug 23, 2017

• Merge pull request #2 from ewels/master

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• New logo

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• fixed syntax and got a successful start

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• Merge pull request #3 from ewels/master

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• Merge branch 'master' of github.com:SciLifeLab/NGI-RNAfusion

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Commits on Sep 4, 2017

• Added tags and other minor tweaks

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Commits on Sep 5, 2017

• sorted out tag naming

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• started on Docker support

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• started on Docker support

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• Merge branch 'master' of github.com:Hammarn/NGI-RNAseq-Fusiondetect

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• sorting out fusioninspector parameters

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• Merge branch 'master' of github.com:Hammarn/NGI-RNAseq-Fusiondetect

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• Dockerfile

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• added fusioninspector to config

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Commits on Sep 8, 2017

• tweaking

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Commits on Sep 14, 2017

• fixed markdown syntax

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Commits on Sep 22, 2017

• Fixing up output file naming

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• Merge branch 'master' of github.com:Hammarn/NGI-RNAfusion

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Commits on Sep 27, 2017

• spelling correction

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Commits on Oct 2, 2017

• added in the . in time requirement

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• removed superfluous params.outdirs

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Commits on Oct 9, 2017

• bumped up the FusionCatcher time requirement

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Commits on Oct 10, 2017

• bumped up the FusionCatcher time requirement

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Commits on Oct 11, 2017

• Merge branch 'master' of github.com:Hammarn/NGI-RNAfusion

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• added fusion_genes_compare.py script process

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Commits on Oct 13, 2017

• finished up requirements for FusionInspector

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Commits on Nov 16, 2017

• updates

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Commits on Dec 18, 2017

• commiting current state fo dockerfile

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• Merge branch 'master' of github.com:Hammarn/NGI-RNAseq-Fusiondetect

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• Dockerfile cleanup

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Commits on Dec 19, 2017

• added in missing line continuation

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• Bring config files in line with other pipelines

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• added base config

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Commits on Jan 12, 2018

• Removed extra dockerfile

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• config updats for rackham

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• removed extra params

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Commits on Jan 22, 2018

• Merge pull request #4 from Hammarn/master

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• Started on support for single end

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• Merge branch 'master' of github.com:Hammarn/NGI-RNAseq-Fusiondetect

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Commits on Jan 23, 2018

• moved around proccess order to make more sense

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• added in missing commands

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Commits on Jan 25, 2018

• bugfixing

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Commits on Jan 30, 2018

• generalized the inputfile grouping

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Commits on Feb 2, 2018

• Decreased the size of the image by removing intermediate files

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Commits on Feb 5, 2018

• docker parasms compatibility

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Commits on Feb 6, 2018

• reference inputs fixing

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• sorted out reference parameters

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• small Readme update

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Commits on Mar 1, 2018

• Merge pull request #5 from Hammarn/master

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• Removed debugging

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• reworked star fusion references checking

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• indentation fix

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• Merge pull request #6 from Hammarn/master

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Commits on Sep 12, 2018

• Upgrade suggestions

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Commits on Sep 13, 2018

• Fixed mistakes in config and main.nf

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• Actually works

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• Updated Dockerfile with conda support

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• Transition to singularity

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• Update project to run with singularity

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• Working singularity

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• Test data

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Commits on Sep 14, 2018

• Merge pull request #11 from matq007/ngi-upgrade

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• Initial template commit

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Commits on Sep 17, 2018

• Merged vanilla TEMPLATE branch into master

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• Removed test data

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• Updated Dockerfile with conda

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Commits on Sep 18, 2018

• Compatable Dockerfile with Singularity

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Commits on Sep 19, 2018

• Implemented STAR-Fusion

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• Implemented Fusion Catcher

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Commits on Sep 21, 2018

• Rearranged Dockerfile

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• Cleanup

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Commits on Sep 25, 2018

• Added GRCh38 genome to the list

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• Fixed GRCh38 path

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Commits on Oct 2, 2018

• Utility for extracting found fusion genes by various tools

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• Added Fusion-Inspector

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• Added Fusion-Inspector version number and cleanup

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Commits on Oct 3, 2018

• Updated transformer usage

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• Removed IGV folder from Fusion-Inspector

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Commits on Oct 4, 2018

• Fixed writting when no fusions are found

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Commits on Oct 5, 2018

• Changed summary structure

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• Generated pretty MultiQC section

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• Updated pipeline structure

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• Merge pull request #1 from matq007/master

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• Merge pull request #2 from nf-core/dev

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• remove branding and add logo

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• Merge branch 'dev' into master

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• Merge pull request #8 from MaxUlysse/master

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• Merge pull request #9 from nf-core/dev

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• Update README.md

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• Merge pull request #10 from nf-core/MaxUlysse-patch-1

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• Merge pull request #11 from nf-core/dev

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Commits on Oct 8, 2018

• Finished transformer for STAR-Fusion (#16)

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• Merge pull request #20 from matq007/issue-16

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Commits on Oct 17, 2018

• Lint positive #15 (#21)

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Commits on Nov 1, 2018

• Testing new setup (#26)

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Commits on Nov 2, 2018

• Implemented ericscript

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Commits on Nov 5, 2018

• Finished Eriscript

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Commits on Nov 6, 2018

• Merge pull request #27 from matq007/issue-4

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• Implemented Pizzly

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Commits on Nov 7, 2018

• Merge pull request #28 from matq007/issue-22

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Commits on Nov 8, 2018

• Implemented Squid

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• Fixed withName in docker.config

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• Merge pull request #30 from matq007/issue-29

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Commits on Nov 10, 2018

• Removed chimerascan

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• Removed tophat and tophat-fusion

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Commits on Nov 11, 2018

• Cleanup

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Commits on Nov 12, 2018

• Merge pull request #32 from matq007/dev

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Commits on Nov 15, 2018

• Boilerplate

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Commits on Nov 20, 2018

• Swapped gene fusions are not the same

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• Fixed libcrypto issue

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• Moved files around on Uppmax

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Commits on Nov 22, 2018

• Merge pull request #33 from matq007/dev

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• Merge branch 'dev' of https://github.com/nf-core/rnafusion into issue-23

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Commits on Nov 26, 2018

• Implementing annotation for squid

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• Implemented squid with annotation

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• Removed pandas package from dependencies

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Commits on Nov 27, 2018

• Merge pull request #35 from matq007/issue-23

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Commits on Dec 18, 2018

• Implemented custom summary report with some rich visualization (#36)

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• Passing builds (#37)

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Commits on Jan 5, 2019

• Minor fixes before release (#38)

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Commits on Jan 7, 2019

• Updated testing parameter (#39)

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• Added documentation (#40)

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Commits on Jan 8, 2019

• Doc improvement and munin configuration (#41)

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Commits on Jan 10, 2019

• Setup for munin (#42)

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• Bumping version to 1.0 (#43)

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• Merge pull request #44 from nf-core/dev

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Commits on Jan 11, 2019

• Fixed CPU parameters for ericscript and pizzly (#46)

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• Merge pull request #47 from nf-core/dev

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Commits on Jan 14, 2019

• Added author and year to MIT LICENCE

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• Refactored configurations

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• Removing shub:// and replacing it with docker://

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• Updated commit tag for gdown.pl

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• Cleanup of variables

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• Refactoring singleEnd condition and updated documentation

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• Increased time-limit for tools

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• Improved when condition for singleEnd

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• Condition bug on squid

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• Updated README and usage docs

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Commits on Jan 15, 2019

• Updated time-limits

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• Fix: smaller report summary

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• Removed old render function

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• Updated singularity image download script with docs

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• Added destination parameter to download-references.sh

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Commits on Jan 16, 2019

• Renamed NGI-RNAfusion to nfcore/rnafusion in all Dockerfiles

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• Updated README

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Commits on Jan 17, 2019

• Added tool cutoff parameter

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• Increased max_cpus in base.config, checking for max_cpus in processes now

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• Removing private uppmax-devel.config

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• Updated munin configurations

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• Mentioned nf-core/configs in adding your own configuration

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• Renamed tools.md to references.md, updated README

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• Updated troubleshooting

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• Added ASCII nfcore logo into help

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Commits on Jan 18, 2019

• Added tool_cutoff param and updated description

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• Updated configurations

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• Updated test profile to check just for syntax

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• Merged summary-report into main container

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• Removing testing Dockerfiles

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• Huge update on main.nf

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• Supports only one single/paired-end read, no batch mode for now

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Commits on Jan 20, 2019

• Parsing filtered output from pizzly

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• Added FusionGDB

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• Updated output documentation

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• Updated output documentation

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Commits on Jan 21, 2019

• Fixed linting on markdown

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Commits on Jan 23, 2019

• Updated testing

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• Following PEP-8 guidelines

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• Fixed coloring on ditribution chart

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• Processing filtered fusions from Ericscript

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• Fixed travis

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• Fixing travis again

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• Fixing Travis again

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• Fixing Travis again

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• Fixing Travis again

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• Fixed indent on help command

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• Testing markdownlint

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• Add sudo permissions to apt-get

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Commits on Jan 24, 2019

• Updated CHANGELOG.md

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• Markdownlint check the whole project not only docs folder

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Commits on Jan 29, 2019

• Added docs to the python code

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• Added pylint checking of python scripts

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Commits on Jan 31, 2019

• Added MIT badge

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• Transformer is not throwing error any more just prints error messages

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• Added process for building STAR index

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• Added star_index into test configuration

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• Using markdownlint configuration and structure from nf-core/tools solution

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• Cleanup

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• Updated documentation for usage

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• Added new GUI configuration for parameters

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Commits on Feb 4, 2019

• Specified params for reads in STAR-Fusion

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Commits on Feb 5, 2019

• Using fusioncatcher from conda hcc channel

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• Deleted Singularity file

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• Add Singularity file back

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