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Documentation improvements #77

Merged
merged 13 commits into from
Nov 4, 2018
Merged

Documentation improvements #77

merged 13 commits into from
Nov 4, 2018

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jfy133
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@jfy133 jfy133 commented Nov 4, 2018 •
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Overall updated documentation and help updated to latest(ish) version

Summary

  • Added list of tools to be installed locally if -profile standard (note still needs to be updated to 2.0.2 specifications`
  • Switched --fasta and --iGenomes documentation sections as the former will be more common in aDNA community.
  • moved now mandatory options to corresponding section
  • renamed (optional) extra data info flags accordingly
  • made adapterRemoval flag descriptions more specific
  • And the usual minor typos.

PR checklist

  • [X ] 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/eager 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

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

jfy133 and others added 10 commits October 14, 2018 14:29
@jfy133
Merge pull request #1 from nf-core/master
f596fff 
Pull latest updates
@jfy133
Switched and descriptions, as I think people are more likely to use t…
40ceca9 
…heir own lab's default references than iGenomes
@jfy133
Added list of used software
7779a03
@jfy133
Merge pull request #2 from nf-core/dev
c33c7ce 
Syncing upstream changes
@jfy133
Merge pull request #4 from jfy133/master
087cd6e 
Upstream change syncing
@jfy133
Update README.md
6d21438
@jfy133
Updated help message
3c75edd 
1) moved some previously optional but now mandatory arguments to correct section
2) added --pairedEnd message
3) renamed 'options' to be more specific (as referring to data type)
4) specified `--clip_forward_*` flag refers to sequence
@jfy133
Fixed small typo
2cd4e60
@jfy133
Removed a few leftover template indicators
aa3a182
@jfy133
Removed a few leftover template indicators
52e999c
apeltzer
apeltzer approved these changes Nov 4, 2018
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Thank you for this :-)

@jfy133
Clean up table of contents
81ff959 
Very long table of contents and inconsistent depth makes hard to find correct section quickly
@jfy133
Fixed link typo
06fa392
@jfy133
Second link fix
3b7df22
@apeltzer apeltzer merged commit 97ea5f8 into nf-core:dev Nov 4, 2018
@apeltzer apeltzer mentioned this pull request Dec 9, 2018
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@apeltzer apeltzer apeltzer approved these changes

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