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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

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apeltzer
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@apeltzer apeltzer commented Dec 2, 2019

This is the PR for the very first release of nf-core/scrnaseq.

The workflow features 3 different options:

  • Kallisto / Bustools
  • STARsolo
  • Salmon Alevin + AlevinQC

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

apeltzer and others added 30 commits June 23, 2019 16:00
@apeltzer
Move runOptions for Docker accordingly
639f9cf
@apeltzer
Adding in Olga to authors too
91095e6
@apeltzer
Add some stuff to changelog
f646c6a
@apeltzer
Add in t2g tool to generate transcripts to genes list
d68b5fe
@apeltzer
Add build_gene_map
4ed5a5f
@apeltzer
Lowercase for whitelist
d022819
@apeltzer
Adding in Kallisto + Bustools etc pp
d553b81
@apeltzer
Add Testcase for Kallisto Part
70dbee1
@apeltzer
Add Kallisto to checks
f2d892a
@apeltzer
Chmod +x
decfd00
@apeltzer
Fix checks for kallisto workflow
6422e6d
@apeltzer
Fix name
da6c337
@apeltzer
Add bustools correct and sort
6fc14bb
@apeltzer
Remove params stuff
9d0c9e6
@apeltzer
Default is V3
eafa46b
@apeltzer
Add some comments to main.nf
05100e4
@apeltzer
Try testing only the kallisto one
bc8ae97
@apeltzer
Add some more defaults
edddfe0
@apeltzer
Remove printing for debugging
128cc3d
@apeltzer
Add software versions scraping
602cf37
@apeltzer
scraping works now fine
ba6f7b4
@apeltzer
Revert back to correct and sort
e20e96e
@apeltzer
Use proper whitelist file (uncompressed)
68be869
@apeltzer
Add summary details on data type + chemistry
99b7993
@apeltzer
Use V2 chemistry
763c818
@apeltzer
Add Kallisto to multiqc
dd33f18
@apeltzer
Add ability to skip correction phase
6f41d55
@apeltzer
Merge pull request #8 from apeltzer/kallisto-bustools
dcd3264 
[Feature]: Add Kallisto + BUSTools Workflow Parts
@olgabot
use if instead of when
8d7dd41
@olgabot
Wrap star alignment in 'if' rather than 'when'
7d2319e
@apeltzer apeltzer requested a review from a team December 2, 2019 21:05
@apeltzer apeltzer added this to Reviews needed in hackathon-scilifelab-2019 Dec 2, 2019
@apeltzer
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apeltzer commented Dec 3, 2019

This is only docker cloud behaving odd.

olgabot
olgabot requested changes Dec 6, 2019
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Awesome work! Some nitpicky changes about documentation and variable names, plus questions about minimum nextflow versions.

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apeltzer and others added 3 commits December 6, 2019 16:58
@apeltzer @olgabot
Apply suggestions from code review
8263d21 
Co-Authored-By: Olga Botvinnik <olga.botvinnik@gmail.com>
@apeltzer
Consistency!
cdfb212
@apeltzer
Add remaining issues
12f1e90
@apeltzer apeltzer requested review from olgabot and a team December 6, 2019 16:07
olgabot
olgabot approved these changes Dec 6, 2019
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Whooo! Great work!

@apeltzer apeltzer merged commit 884e541 into master Dec 9, 2019
hackathon-scilifelab-2019 automation moved this from Reviews needed to Done Dec 9, 2019
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