This updates and fills in the templated parts of the pull request template.
In addition to removing the template text and cleaning up a few markdown quirks, I overhauled the Testing Results section. My impression is that users (myself included) almost never completely fill out the existing "Case 1: sample, input csv, ..." table (if we do at all). I switched instead to "requiring" the path to and the last few lines of the NFTest log file, or a justification of why testing isn't required (for example, this PR doesn't require testing because it's a documentation-only change). If/when anyone cares to go digging, the NFTest logfile has the details of the test run and is stored adjacent to the output files themselves.
This is functionally identical to what I wrote up for #36, and I think it's simultaneously more informative and more usable, but I welcome any feedback on it! If everyone likes it I think this (or something like it) could be a good template to apply to other repos making use of NFTest.
[x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
[x] I have set up or verified the branch protection rule following the github standards before opening this pull request.
[ ] I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
already, or do not wish to be listed. (This acknowledgement is optional.)
[ ] ~I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.~ I don't want to conflict with #36 for now
[ ] I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)
[ ] I have tested the pipeline on at least one A-mini sample.
This updates and fills in the templated parts of the pull request template.
In addition to removing the template text and cleaning up a few markdown quirks, I overhauled the
Testing Results
section. My impression is that users (myself included) almost never completely fill out the existing "Case 1: sample, input csv, ..." table (if we do at all). I switched instead to "requiring" the path to and the last few lines of the NFTest log file, or a justification of why testing isn't required (for example, this PR doesn't require testing because it's a documentation-only change). If/when anyone cares to go digging, the NFTest logfile has the details of the test run and is stored adjacent to the output files themselves.This is functionally identical to what I wrote up for #36, and I think it's simultaneously more informative and more usable, but I welcome any feedback on it! If everyone likes it I think this (or something like it) could be a good template to apply to other repos making use of NFTest.
Checklist
[x] I have read the code review guidelines and the code review best practice on GitHub check-list.
[x] I have reviewed the Nextflow pipeline standards.
[x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
[x] I have set up or verified the branch protection rule following the github standards before opening this pull request.
[ ] I have added my name to the contributors listings in the
manifest
block in thenextflow.config
as part of this pull request, am listed already, or do not wish to be listed. (This acknowledgement is optional.)[ ] ~I have added the changes included in this pull request to the
CHANGELOG.md
under the next release version or unreleased, and updated the date.~ I don't want to conflict with #36 for now[ ] I have updated the version number in the
metadata.yaml
andmanifest
block of thenextflow.config
file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)[ ] I have tested the pipeline on at least one A-mini sample.