Add slightly modified version of GATK3 github issue template #4796

ldgauthier · 2018-05-22T13:22:32Z

Text edits are welcome. I tried to split the difference between being a pushover and fully expressing my frustration.

lbergelson · 2018-05-22T15:27:54Z

.github/ISSUE_TEMPLATE.md

+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above;
+- Use a **concise** yet **descriptive** title;
+- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate;
+- If the issue will be added to the public tracker (using the `public` label), it must conform to [these guidelines](http://gatkforums.broadinstitute.org/dsde/discussion/6801/guidelines-for-tagging-issues-with-the-public-tag#latest);


I don't think this line about the public issue tracker is relevant.

lbergelson · 2018-05-22T15:36:30Z

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,55 @@
+### Instructions
+
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));


Maybe a few sentences of prefix before diving in? Something like `The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc should be asked on the official support forum. "

lbergelson · 2018-05-22T15:39:17Z

.github/ISSUE_TEMPLATE.md

+
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above;
+- Use a **concise** yet **descriptive** title;


I would probably add a line suggesting to first search the issues to see if there's an existing ticket.

ldgauthier · 2018-05-23T13:23:16Z

Done. Anyone else want to take a look? Maybe @droazen or @sooheelee ?

codecov-io · 2018-05-23T14:28:41Z

Codecov Report

Merging #4796 into master will decrease coverage by 0.045%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #4796       +/-   ##
===============================================
- Coverage     80.111%   80.066%   -0.045%     
- Complexity     17442     18215      +773     
===============================================
  Files           1083      1090        +7     
  Lines          63165     66368     +3203     
  Branches       10193     10983      +790     
===============================================
+ Hits           50602     53138     +2536     
- Misses          8574      9108      +534     
- Partials        3989      4122      +133

Impacted Files	Coverage Δ	Complexity Δ
...r/dataSources/cosmic/CosmicFuncotationFactory.java	`59.184% <0%> (-17.054%)`	`24% <0%> (+3%)`
...e/hellbender/tools/funcotator/FuncotatorUtils.java	`64.925% <0%> (-14.435%)`	`176% <0%> (+25%)`
...dataSources/gencode/GencodeFuncotationFactory.java	`73.673% <0%> (-8.661%)`	`182% <0%> (+32%)`
.../utils/read/markduplicates/LibraryIdGenerator.java	`91.228% <0%> (-3.216%)`	`27% <0%> (+13%)`
...forms/markduplicates/MarkDuplicatesSparkUtils.java	`87.64% <0%> (-2.147%)`	`72% <0%> (+2%)`
...der/tools/walkers/mutect/M2ArgumentCollection.java	`93.939% <0%> (-0.178%)`	`5% <0%> (+2%)`
...a/org/broadinstitute/hellbender/utils/Trilean.java	`100% <0%> (ø)`	`3% <0%> (+2%)`	⬆️
...otypecaller/HaplotypeCallerArgumentCollection.java	`100% <0%> (ø)`	`2% <0%> (ø)`	⬇️
...broadinstitute/hellbender/engine/ReadsContext.java	`100% <0%> (ø)`	`13% <0%> (+4%)`	⬆️
...s/spark/sv/discovery/SvDiscoveryInputMetaData.java	`100% <0%> (ø)`	`8% <0%> (+6%)`	⬆️
... and 49 more

lbergelson · 2018-05-23T14:49:10Z

.github/ISSUE_TEMPLATE.md

+### Instructions
+
+The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc should be asked on the [official support forum](http://gatkforums.broadinstitute.org/gatk).
+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.;


there are a bunch of semicolons that don't belong

lbergelson · 2018-05-23T14:49:18Z

.github/ISSUE_TEMPLATE.md

+
+The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc should be asked on the [official support forum](http://gatkforums.broadinstitute.org/gatk).
+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.;
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));


2 semicolons on this line.

lbergelson · 2018-05-23T14:49:27Z

.github/ISSUE_TEMPLATE.md

+The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc should be asked on the [official support forum](http://gatkforums.broadinstitute.org/gatk).
+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.;
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above;


lbergelson · 2018-05-23T14:49:32Z

.github/ISSUE_TEMPLATE.md

+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.;
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above;
+- Use a **concise** yet **descriptive** title;


lbergelson · 2018-05-23T14:49:38Z

.github/ISSUE_TEMPLATE.md

+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above;
+- Use a **concise** yet **descriptive** title;
+- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate;


lbergelson · 2018-05-23T14:50:22Z

...adinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculatorUnitTest.java

@@ -170,6 +170,25 @@ public void testManyRefSamplesDontKillGoodVariant() {
        }
    }

+    @Test


I don't think you meant to include this test.

I wondered why I didn't have to stash the test when I checked out my other branch.

I removed the semicolons. Maybe that was what kept the old template from actually being rendered in markdown.

droazen

Looks good to me -- trivial comments only. Merge after addressing them.

droazen · 2018-05-24T19:20:05Z

.github/ISSUE_TEMPLATE.md

+The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc should be asked on the [official support forum](http://gatkforums.broadinstitute.org/gatk).
+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only -- for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues))
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results or generally any question that does not fit the categories above


"fit" -> "fit into"

Also, add oxford comma :)

droazen · 2018-05-24T19:22:13Z

.github/ISSUE_TEMPLATE.md

+
+### Affected version(s)
+- [ ] Latest public release version [version?]
+- [ ] Latest development/master branch as of [date of test?]


"development/master" -> "master" (we don't have a permanent develop branch in GATK4)

magicDGS · 2018-05-25T08:20:53Z

.github/ISSUE_TEMPLATE.md

+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only -- for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues))
+- Consider if your "issue" is better addressed on the GATK forum: http://gatkforums.broadinstitute.org/gatk  Post there if you have questions about expected tool behavior, output format, unexpected results, or generally any question that does not fit into the categories above
+- Use a **concise** yet **descriptive** title
+- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate


Templates are focused on tool(s), but there isn't any guideline for engine suggestions - this is important for developers using GATK4 as a framework (that's my case).

If you're savvy enough to make feature requests for the engine, you probably can write a good issue without a template. :-) @droazen or @lbergelson thoughts?

I see your point @ldgauthier, but I think @magicDGS's point is worth addressing. The issue template is one of the first exposures people trying to contribute something have, so if it's an awkward match to what they're trying to tell us it is sort of dispiriting.

What if we clarify it by changing the wording to Affected Tools or Classes in the various places tools are mentioned . It's a bit more verbose but it makes it clear that it's either for top level bugs with tools or for API / internal bugs.

@magicDGS Would that make it seem better for your use case? Or do you have a different suggestion for an alternative template or something like that?

I am ok with both the tool-driven and your proposal - I was just wondering what is the best way to submit an issue/proposal for the engine (as I do often), because I am planning to follow as much as possible the templates. I think that the addition of "Classes" might be good for letting know people that the template is the same for engine/tools.

Thanks for considering my opinion!

lbergelson · 2018-05-25T20:00:50Z

.github/ISSUE_TEMPLATE.md

+
+The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc. should be asked on the [official support forum](http://gatkforums.broadinstitute.org/gatk).
+- Search the existing github issues to see if your issue (or something similar) has already been reported.  If the issue already exists, you may comment there to inquire about the progress.
+- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only -- for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues))


maybe tool gatk docs -> javadoc ?

By the way, I guess that the repository is private - it might be a good idea to mention it, because I was trying to access and I was wondering why it didn't work. I can't submit an issue about forum docs, but I guess that I would not realize if there is an issue there.

Oh. I didn't realize that. We should not link to a private repository.

Expanded issue types to include Java classes as well as GATK tools

ldgauthier · 2018-05-29T15:51:45Z

back to @lbergelson

droazen

👍 merging

Add slightly modified version of GATK3 github issue template

9029ace

lbergelson reviewed May 22, 2018

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Incorporating Louis's suggestions

576b5a9

lbergelson reviewed May 23, 2018

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Cleanup semicolons and remove errant file

fbc0d74

droazen approved these changes May 24, 2018

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droazen assigned ldgauthier May 24, 2018

Final cleanup

d336fc2

magicDGS reviewed May 25, 2018

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lbergelson reviewed May 25, 2018

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Removed reference to private dsde-docs repo

934d7e6

Expanded issue types to include Java classes as well as GATK tools

droazen approved these changes Jun 5, 2018

View reviewed changes

droazen merged commit 8763c57 into master Jun 5, 2018

droazen deleted the ldg_githubIssueTemplate branch June 5, 2018 18:59

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Add slightly modified version of GATK3 github issue template #4796

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		@@ -0,0 +1,55 @@
		### Instructions

		- Determine whether your issue is a bug report, a feature request, or a documentation request (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues));

@@ @@ -170,6 +170,25 @@ public void testManyRefSamplesDontKillGoodVariant() { @@
                       }
                   }
+                  @Test

Add slightly modified version of GATK3 github issue template #4796

Add slightly modified version of GATK3 github issue template #4796

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