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JOSS review comments -- redux #109

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Aug 26, 2020
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c208a36
moved install dependencies bit
lincoln-harris Aug 24, 2020
8fdf8a3
updated USAGE.md path
lincoln-harris Aug 24, 2020
18fd26c
added adnl explanation for report_coverage option
lincoln-harris Aug 24, 2020
401e8e9
fixed csv vs json output issues
Aug 24, 2020
865d0ea
merge branch 'joss-review-redux' of https://github.com/czbiohub/cereb…
Aug 24, 2020
5f39fe7
updated issue report href
lincoln-harris Aug 24, 2020
3b0fbe3
updated report_coverage explanation
lincoln-harris Aug 24, 2020
286a306
further updates to USAGE.md
lincoln-harris Aug 24, 2020
d2b42c9
to -> and
lincoln-harris Aug 24, 2020
f6d1b69
nl
lincoln-harris Aug 24, 2020
f22ba7b
proper test VCF path in USAGE.md
lincoln-harris Aug 24, 2020
966dffc
moved windows exception in README.md
lincoln-harris Aug 24, 2020
bb83815
experimental -> tumor
lincoln-harris Aug 24, 2020
ad8485c
update paper.md
lincoln-harris Aug 24, 2020
b048b8f
update readme
lincoln-harris Aug 24, 2020
783b9ed
`germline-filter`
lincoln-harris Aug 24, 2020
6ef4dde
vs -> vs.
lincoln-harris Aug 24, 2020
f5edfe6
commented out types comparison stdout in utils.py
Aug 24, 2020
8a17b04
changed up germline filter option names
Aug 24, 2020
02aac26
update README
lincoln-harris Aug 24, 2020
b1c596a
small change to gf docstring
Aug 24, 2020
7dc711d
renamed gl-filt test dirs
Aug 24, 2020
04bc3c9
updated maynard ref
lincoln-harris Aug 25, 2020
77aba3c
docker (recommended)
lincoln-harris Aug 25, 2020
1b5d316
2019->2020
lincoln-harris Aug 25, 2020
1cabcf4
introduced WSL
lincoln-harris Aug 25, 2020
824fed2
added bio-informatics classifier in setup.py
Aug 25, 2020
b342788
cerebra -> `cerebra`
lincoln-harris Aug 25, 2020
f874165
adding separate Dependencies and Install (users vs developers) sections
lincoln-harris Aug 25, 2020
d9e5acc
dependencies hlink
lincoln-harris Aug 25, 2020
4af8344
pypi not recommended
lincoln-harris Aug 25, 2020
9368f13
`venv`
lincoln-harris Aug 25, 2020
77218cd
see CONTRIBUTING.md for more
lincoln-harris Aug 25, 2020
7a171b2
pypi install is not recommended
lincoln-harris Aug 25, 2020
9086622
updated INSTALL.md
lincoln-harris Aug 25, 2020
208825b
updated dependencies hlink
lincoln-harris Aug 25, 2020
1bd74dd
bolded
lincoln-harris Aug 25, 2020
d5c35b2
tumor/normal in USAGE.md
lincoln-harris Aug 25, 2020
daa2040
updates to USAGE.md
lincoln-harris Aug 25, 2020
916645d
wip
lincoln-harris Aug 25, 2020
7e20fd5
maynard 2020
lincoln-harris Aug 25, 2020
276b177
removed -e from makefile
lincoln-harris Aug 25, 2020
4b1889b
adding in issue templates
Aug 25, 2020
cee518b
update bugreport
lincoln-harris Aug 25, 2020
529e6c6
update bugreport
lincoln-harris Aug 25, 2020
3510bb8
removing bug_report.md and feature_request.md
lincoln-harris Aug 25, 2020
451e1bd
uncommented adnl sections in .travis.yml
lincoln-harris Aug 25, 2020
ba58b0a
changed pip install instruct in developer install
lincoln-harris Aug 25, 2020
358e87b
pip install in readme
lincoln-harris Aug 25, 2020
d6cb644
flake8 -> `flake8`
lincoln-harris Aug 25, 2020
6f33854
removed local dev guidelines from contributing.md
lincoln-harris Aug 25, 2020
9815ea6
changes to contributing.md
lincoln-harris Aug 25, 2020
a8c24ff
got rid of make coverage in .travis.yml
lincoln-harris Aug 25, 2020
d4a91f5
some changers
lincoln-harris Aug 26, 2020
d40de09
some spelling mistakes
lincoln-harris Aug 26, 2020
53d83b6
various spelling changes to README
lincoln-harris Aug 26, 2020
b8ae7d1
some revisions to REAME
lincoln-harris Aug 26, 2020
5e83fa5
changed intro to README
lincoln-harris Aug 26, 2020
dbae4da
lint
lincoln-harris Aug 26, 2020
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adding in issue templates
Lincoln Harris committed Aug 25, 2020
commit 4b1889bac1dad4008fe285d86e6e21429aaf523f
38 changes: 38 additions & 0 deletions docs/bug_report.md
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---
name: Bug report
about: Create a report to help us improve
title: ''
labels: ''
assignees: ''

---

**Describe the bug**
A clear and concise description of what the bug is.

**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

**Expected behavior**
A clear and concise description of what you expected to happen.

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Desktop (please complete the following information):**
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]

**Smartphone (please complete the following information):**
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]

**Additional context**
Add any other context about the problem here.
20 changes: 20 additions & 0 deletions docs/feature_request.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
---
name: Feature request
about: Suggest an idea for this project
title: ''
labels: ''
assignees: ''

---

**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**
A clear and concise description of what you want to happen.

**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.

**Additional context**
Add any other context or screenshots about the feature request here.