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0.1.0 Release #23

Merged
merged 155 commits into from
Aug 14, 2024
Merged

0.1.0 Release #23

merged 155 commits into from
Aug 14, 2024

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sgsutcliffe
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Initial release of staramrnf, or staramr nextflow pipeline, is a nextflow wrapper of staramr. Doing some last set of testing before the release into main.

PR checklist

  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Tested on Azure
  • Tested in IRIDA Next
  • Document an additonal tests

apetkau and others added 30 commits May 23, 2024 08:39
@apetkau
Added test data
d91f9a2
@apetkau
Add other needed files for tests
55e1dd9
@apetkau
Merge pull request #5 from phac-nml/test-data
f39f598 
Added test data
@apetkau
Merge pull request #6 from phac-nml/fix-tests
f1b2f99 
Add other needed files for tests
@sgsutcliffe
Updated for nf-core lint
ef84928
@sgsutcliffe
Updated for nf-core lint
07922ff
@sgsutcliffe
nf-core lint fix
3a4b3a1
@sgsutcliffe
Fixed with prettier
3e852da
@sgsutcliffe
linting fix
5362710
@sgsutcliffe
Updated nf-core to version 2.14.1
a231a12
@sgsutcliffe
Merge pull request #7 from phac-nml/fix-CI-linting
aac342d 
Fix CI linting
@sgsutcliffe
Add nf-test CI
2c30661
@sgsutcliffe
Add nf-test CI
3e8dd46
@sgsutcliffe
Fix input of test.config for test-profile
23cf247
@sgsutcliffe
Change the input path to URL
87990a5
@sgsutcliffe
Removed output directory default setting for test profile
ff38746
@sgsutcliffe
Remove files added during troubleshooting fix of nf-test
29c4382
@sgsutcliffe
Correct change
eddc6da
@sgsutcliffe
Change input from local file to URL
8f36517
@sgsutcliffe
Merge pull request #8 from phac-nml/setup-CI-nf-test
737deaa 
Setup nf-test CI for pull-requests
@sgsutcliffe
Updated and removed nf-core branding
497b77b
@sgsutcliffe
Removed docs until we add staramr-nextflow pipeline files
88f0870
@sgsutcliffe
Remove reference to the nf-core/tests-datasets repository
dbf793d
@sgsutcliffe
Fixed prettier
a4c23bb
@sgsutcliffe
Keeping for now, as it breaks nf-test
790ca65
@sgsutcliffe
Modification broke the nf-test CI
024f07d
@sgsutcliffe
Return to template version
ecea6ab
@sgsutcliffe
Added IRIDA Next JSON output file
58ba5b7
@sgsutcliffe
Update name of repository
94dc37f
@sgsutcliffe
Fixed repository name
150e74a
sgsutcliffe and others added 26 commits August 12, 2024 10:02
@sgsutcliffe
Updated authors in manifest
416492d
@sgsutcliffe
Typo in homepage URL
b41700c
@sgsutcliffe
Change branch link to main
b5d6426
@sgsutcliffe
Removed remaining config urls to main
4fe0406
@sgsutcliffe
Merge pull request #22 from phac-nml/prefix-to-metadata-field
b78d58b 
Resolves #17 Add "StarAMR" prefix to each metadata field
@sgsutcliffe
Found another vestigal file of subworkflows/input_check.nf
d2e71ca
@sgsutcliffe
Removed spades module
befceb4
@sgsutcliffe
Forgot to commit removal of spades to modules.json
6454afe
@sgsutcliffe
Wrong file commited for spades modules.json commit
6cfbe97
@sgsutcliffe
Improve sentence clarity
d3b3ac8
@sgsutcliffe
Fixed typo in URL
9c52b62
@sgsutcliffe
Add links to database references
788f0f6
@sgsutcliffe
Fixed URLS
48a9c71
@sgsutcliffe
Changed nf-core links accidently to main
3d6e79a
@sgsutcliffe
Add default branch to manifest
bb623e8
@sgsutcliffe
Made prettier
3d67349
@sgsutcliffe
Merge pull request #20 from phac-nml/update-docs
878635f 
Updated docs for release
@sgsutcliffe
Update CHANGELOG.md Release Date
21b434c
@sgsutcliffe
Update CHANGELOG.md
f08010f
@sgsutcliffe
Prettier fix
d53d343
@sgsutcliffe
Added two additional metadata tags and nf-test asserts
bdd45d3
@sgsutcliffe
Merge pull request #25 from phac-nml/add-metadata-field
1e29738 
Added two additional metadata tags and nf-test asserts
@sgsutcliffe
Modified the output files to have staramr file extension
dc2489d
@sgsutcliffe
Modified documentation regarding pipeline output
248f10b
@sgsutcliffe
Modified regex for file naming
fa6f128
@sgsutcliffe
Merge pull request #27 from phac-nml/modify-output-filenames
1f7d602 
Resolves #26 Modify output files with `staramr`
apetkau
apetkau requested changes Aug 14, 2024
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Looks great. Just one small change prior to release 😄

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apetkau
apetkau approved these changes Aug 14, 2024
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Looks great to me.

@sgsutcliffe sgsutcliffe merged commit 61de9f9 into main Aug 14, 2024
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@apetkau apetkau apetkau approved these changes

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@sgsutcliffe @apetkau