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PR for 1.0.0 release #17

Merged
merged 138 commits into from
Dec 9, 2019
Merged

PR for 1.0.0 release #17

merged 138 commits into from
Dec 9, 2019

Commits on Jun 23, 2019

  1. Move runOptions for Docker accordingly

    @apeltzer
    apeltzer committed Jun 23, 2019
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  2. Adding in Olga to authors too

    @apeltzer
    apeltzer committed Jun 23, 2019
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  3. Add some stuff to changelog

    @apeltzer
    apeltzer committed Jun 23, 2019
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  4. Add in t2g tool to generate transcripts to genes list

    @apeltzer
    apeltzer committed Jun 23, 2019
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  5. Add build_gene_map

    @apeltzer
    apeltzer committed Jun 23, 2019
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  6. Lowercase for whitelist

    @apeltzer
    apeltzer committed Jun 23, 2019
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  7. Adding in Kallisto + Bustools etc pp

    @apeltzer
    apeltzer committed Jun 23, 2019
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  8. Add Testcase for Kallisto Part

    @apeltzer
    apeltzer committed Jun 23, 2019
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  9. Add Kallisto to checks

    @apeltzer
    apeltzer committed Jun 23, 2019
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  10. Chmod +x

    @apeltzer
    apeltzer committed Jun 23, 2019
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  11. Fix checks for kallisto workflow

    @apeltzer
    apeltzer committed Jun 23, 2019
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  12. Fix name

    @apeltzer
    apeltzer committed Jun 23, 2019
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  13. Add bustools correct and sort

    @apeltzer
    apeltzer committed Jun 23, 2019
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  14. Remove params stuff

    @apeltzer
    apeltzer committed Jun 23, 2019
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  15. Default is V3

    @apeltzer
    apeltzer committed Jun 23, 2019
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  16. Add some comments to main.nf

    @apeltzer
    apeltzer committed Jun 23, 2019
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  17. Try testing only the kallisto one

    @apeltzer
    apeltzer committed Jun 23, 2019
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  18. Add some more defaults

    @apeltzer
    apeltzer committed Jun 23, 2019
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  19. Remove printing for debugging

    @apeltzer
    apeltzer committed Jun 23, 2019
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  20. Add software versions scraping

    @apeltzer
    apeltzer committed Jun 23, 2019
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  21. scraping works now fine

    @apeltzer
    apeltzer committed Jun 23, 2019
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  22. Revert back to correct and sort

    @apeltzer
    apeltzer committed Jun 23, 2019
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  23. Use proper whitelist file (uncompressed)

    @apeltzer
    apeltzer committed Jun 23, 2019
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  24. Add summary details on data type + chemistry

    @apeltzer
    apeltzer committed Jun 23, 2019
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  25. Use V2 chemistry

    @apeltzer
    apeltzer committed Jun 23, 2019
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  26. Add Kallisto to multiqc

    @apeltzer
    apeltzer committed Jun 23, 2019
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Commits on Jun 24, 2019

  1. Add ability to skip correction phase

    @apeltzer
    apeltzer committed Jun 24, 2019
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Commits on Jun 25, 2019

  1. Merge pull request #8 from apeltzer/kallisto-bustools 

    [Feature]: Add Kallisto + BUSTools Workflow Parts
    @apeltzer
    apeltzer committed Jun 25, 2019
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Commits on Jun 27, 2019

  1. use if instead of when

    @olgabot
    olgabot committed Jun 27, 2019
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  2. Wrap star alignment in 'if' rather than 'when'

    @olgabot
    olgabot committed Jun 27, 2019
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  3. Set star_log to empty if not used

    @olgabot
    olgabot committed Jun 27, 2019
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  4. whitespace/newlines for readability

    @olgabot
    olgabot committed Jun 27, 2019
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  5. Can't have multiline single quoted strings

    @olgabot
    olgabot committed Jun 27, 2019
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  6. Please keep the groovy/nxf style

    @apeltzer
    apeltzer committed Jun 27, 2019
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  7. Add smaller whitelist file for simple testing purposes

    @apeltzer
    apeltzer committed Jun 27, 2019
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  8. Add testing profile for testing purposes of kallisto

    @apeltzer
    apeltzer committed Jun 27, 2019
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  9. Adjust the testcase for kallisto accordingly

    @apeltzer
    apeltzer committed Jun 27, 2019
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  10. Remove the correction from bustools for testing

    @apeltzer
    apeltzer committed Jun 27, 2019
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  11. Try auto for tmp files

    @apeltzer
    apeltzer committed Jun 27, 2019
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Commits on Jul 4, 2019

  1. use tee to write separate log file and .command.log

    @olgabot
    olgabot committed Jul 4, 2019
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Commits on Jul 24, 2019

  1. Get --aligner star and --aligner kallisto to start working

    @olgabot
    olgabot committed Jul 24, 2019
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  2. Build STAR from source

    @olgabot
    olgabot committed Jul 24, 2019
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  3. Autosave commit created on Wed Jul 24 16:32:38 PDT 2019.

    @olgabot
    olgabot committed Jul 24, 2019
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Commits on Jul 25, 2019

  1. Fix curlybraces

    @olgabot
    olgabot committed Jul 25, 2019
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Commits on Aug 1, 2019

  1. Fixing alevinqc stuff

    @apeltzer
    apeltzer committed Aug 1, 2019
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  2. Fixing matplotlib version

    @apeltzer
    apeltzer committed Aug 1, 2019
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  3. Drop STAR

    @apeltzer
    apeltzer committed Aug 1, 2019
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  4. Add test for STARsolo

    @apeltzer
    apeltzer committed Aug 1, 2019
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  5. Adding in test profile for STARsolo

    @apeltzer
    apeltzer committed Aug 1, 2019
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  6. Fix error message

    @apeltzer
    apeltzer committed Aug 1, 2019
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  7. Some more documentation

    @apeltzer
    apeltzer committed Aug 1, 2019
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  8. alevinqc recipe updated on bioconda now

    @apeltzer
    apeltzer committed Aug 1, 2019
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Commits on Aug 5, 2019

  1. Fix alevinqc

    @apeltzer
    apeltzer committed Aug 5, 2019
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Commits on Sep 5, 2019

  1. Bump bustools

    @apeltzer
    apeltzer committed Sep 5, 2019
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Commits on Sep 10, 2019

  1. Bump environment to latest tool versions

    @apeltzer
    apeltzer committed Sep 10, 2019
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  2. Fix gz input handling for kallisto gene_map

    @apeltzer
    apeltzer committed Sep 10, 2019
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  3. Add logo properly

    @apeltzer
    apeltzer committed Sep 10, 2019
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  4. Add logo to readme fix #2

    @apeltzer
    apeltzer committed Sep 10, 2019
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Commits on Sep 11, 2019

  1. Make the stuff pass again

    @apeltzer
    apeltzer committed Sep 11, 2019
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  2. Unzip GZ fasta input too

    @apeltzer
    apeltzer committed Sep 11, 2019
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  3. Fixing bustools handling code

    @apeltzer
    apeltzer committed Sep 11, 2019
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  4. Add in bustools inspect for metrics generation

    @apeltzer
    apeltzer committed Sep 11, 2019
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  5. Fix unzipping automation

    @apeltzer
    apeltzer committed Sep 11, 2019
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  6. Update environment.yml 

    Update and bump version in environment for rebuilding Docker container
    @apeltzer
    apeltzer committed Sep 11, 2019
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  7. Update environment.yml

    @apeltzer
    apeltzer committed Sep 11, 2019
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  8. Tests are working now

    @apeltzer
    apeltzer committed Sep 11, 2019
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  9. Update environment.yml 

    Final bump, all recipes are fine 👍
    @apeltzer
    apeltzer committed Sep 11, 2019
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  10. Fixed methods

    @apeltzer
    apeltzer committed Sep 11, 2019
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  11. Fix lint

    @apeltzer
    apeltzer committed Sep 11, 2019
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  12. Fix tests

    @apeltzer
    apeltzer committed Sep 11, 2019
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  13. Fix tests

    @apeltzer
    apeltzer committed Sep 11, 2019
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  14. Proper testing using new testdata

    @apeltzer
    apeltzer committed Sep 11, 2019
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  15. Add in bustools inspect to get JSON metrics

    @apeltzer
    apeltzer committed Sep 11, 2019
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  16. Subset barcode whitelist

    @apeltzer
    apeltzer committed Sep 11, 2019
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  17. Sane defaults

    @apeltzer
    apeltzer committed Sep 11, 2019
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  18. Try to not correct due to memory requirements

    @apeltzer
    apeltzer committed Sep 11, 2019
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  19. Add hopefully working matrix tests

    @apeltzer
    apeltzer committed Sep 11, 2019
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  20. Add gene maps more properly to main

    @apeltzer
    apeltzer committed Sep 11, 2019
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  21. Oops

    @apeltzer
    apeltzer committed Sep 11, 2019
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Commits on Sep 12, 2019

  1. Try bustools correction off

    @apeltzer
    apeltzer committed Sep 12, 2019
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  2. Add in documentation about kallisto/bustools

    @apeltzer
    apeltzer committed Sep 12, 2019
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  3. Better file outputs

    @apeltzer
    apeltzer committed Sep 12, 2019
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  4. Cleaned up script

    @apeltzer
    apeltzer committed Sep 12, 2019
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  5. Add GitHub Action testing + README polishing

    @apeltzer
    apeltzer committed Sep 12, 2019
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  6. add clause to script

    @apeltzer
    apeltzer committed Sep 12, 2019
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  7. Merge pull request #10 from nf-core/kallisto-bustools 

    [Feature] Kallisto + Bustools WIP
    @apeltzer
    apeltzer committed Sep 12, 2019
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  8. Fix output linting

    @apeltzer
    apeltzer committed Sep 12, 2019
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  9. Try using subset file

    @apeltzer
    apeltzer committed Sep 12, 2019
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  10. Get skipping in place

    @apeltzer
    apeltzer committed Sep 12, 2019
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  11. Adding in sane defaults

    @apeltzer
    apeltzer committed Sep 12, 2019
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  12. Add lots of documentation for usage here

    @apeltzer
    apeltzer committed Sep 12, 2019
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  13. Cleaner main file

    @apeltzer
    apeltzer committed Sep 12, 2019
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  14. Clean docs a bit further [skip ci]

    @apeltzer
    apeltzer committed Sep 12, 2019
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  15. Fixing tests

    @apeltzer
    apeltzer committed Sep 12, 2019
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  16. Mini docs polish

    @apeltzer
    apeltzer committed Sep 12, 2019
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Commits on Nov 14, 2019

  1. Merge pull request #13 from apeltzer/dev 

    Small Updates
    @apeltzer
    apeltzer committed Nov 14, 2019
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  2. Updated deps, bump nxf 19.10

    @apeltzer
    apeltzer committed Nov 14, 2019
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  3. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into kallis… 

    …to-bustools
    @apeltzer
    apeltzer committed Nov 14, 2019
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  4. Merge pull request #15 from apeltzer/kallisto-bustools 

    Getting dev to run
    @apeltzer
    apeltzer committed Nov 14, 2019
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  5. Fix linter

    @apeltzer
    apeltzer committed Nov 14, 2019
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  6. Bump nxf version

    @apeltzer
    apeltzer committed Nov 14, 2019
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Commits on Nov 28, 2019

  1. Fix travis tests, too long for TravisCI + add this to environment.yml

    @apeltzer
    apeltzer committed Nov 28, 2019
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  2. Adjust tests properly

    @apeltzer
    apeltzer committed Nov 28, 2019
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  3. Hopefully fixes all tests

    @apeltzer
    apeltzer committed Nov 28, 2019
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  4. Fix alevinqc

    @apeltzer
    apeltzer committed Nov 28, 2019
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  5. Add 1.0.0 for PR to Master

    @apeltzer
    apeltzer committed Nov 28, 2019
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  6. Fix tests

    @apeltzer
    apeltzer committed Nov 28, 2019
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  7. Cleaning up a little

    @apeltzer
    apeltzer committed Nov 28, 2019
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  8. Polishing (docs, params)

    @apeltzer
    apeltzer committed Nov 28, 2019
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Commits on Dec 2, 2019

  1. Apply suggestions from code review 

    Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
    @apeltzer @maxulysse
    apeltzer and maxulysse committed Dec 2, 2019
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  2. Apply suggestions from code review 

    Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
    @apeltzer @maxulysse
    apeltzer and maxulysse committed Dec 2, 2019
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  3. Drop AWS Batch for now

    @apeltzer
    apeltzer committed Dec 2, 2019
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  4. Snake Case

    @apeltzer
    apeltzer committed Dec 2, 2019
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  5. Apply suggestions from code review 

    Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
    @apeltzer @maxulysse
    apeltzer and maxulysse committed Dec 2, 2019
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  6. FastA -> fasta

    @apeltzer
    apeltzer committed Dec 2, 2019
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  7. Adjust versioning

    @apeltzer
    apeltzer committed Dec 2, 2019
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  8. Drop test_star profile - improve tests

    @apeltzer
    apeltzer committed Dec 2, 2019
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  9. Indentation stuff

    @apeltzer
    apeltzer committed Dec 2, 2019
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  10. Clean up logic

    @apeltzer
    apeltzer committed Dec 2, 2019
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  11. Cleaned up pipeline logic significantly

    @apeltzer
    apeltzer committed Dec 2, 2019
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  12. replace ifs with when

    @apeltzer
    apeltzer committed Dec 2, 2019
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  13. Fix remaining channel operations

    @apeltzer
    apeltzer committed Dec 2, 2019
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  14. Fix missing fonts

    @apeltzer
    apeltzer committed Dec 2, 2019
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  15. Clean up a bit

    @apeltzer
    apeltzer committed Dec 2, 2019
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  16. Clean up configs, sort params

    @apeltzer
    apeltzer committed Dec 2, 2019
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  17. Much more docs

    @apeltzer
    apeltzer committed Dec 2, 2019
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  18. Nicer docs

    @apeltzer
    apeltzer committed Dec 2, 2019
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  19. Nicer summary

    @apeltzer
    apeltzer committed Dec 2, 2019
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  20. Mini cosmetics

    @apeltzer
    apeltzer committed Dec 2, 2019
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  21. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into dev

    @apeltzer
    apeltzer committed Dec 2, 2019
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  22. Fix docs lint

    @apeltzer
    apeltzer committed Dec 2, 2019
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  23. Merge branch 'master' into dev

    @apeltzer
    apeltzer committed Dec 2, 2019
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Commits on Dec 6, 2019

  1. Apply suggestions from code review 

    Co-Authored-By: Olga Botvinnik <olga.botvinnik@gmail.com>
    @apeltzer @olgabot
    apeltzer and olgabot committed Dec 6, 2019
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  2. Consistency!

    @apeltzer
    apeltzer committed Dec 6, 2019
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  3. Add remaining issues

    @apeltzer
    apeltzer committed Dec 6, 2019
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  4. When after output

    @apeltzer
    apeltzer committed Dec 6, 2019
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  5. Drop old matplotlib - new multiqc!

    @apeltzer
    apeltzer committed Dec 6, 2019
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Commits on Dec 9, 2019

  1. Fix usage

    @apeltzer
    apeltzer committed Dec 9, 2019
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