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Deploy dev branch to crazy-corgi #560

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PR checklist

  • 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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

nf-core-bot and others added 30 commits October 8, 2024 12:32
@nf-core-bot
Template update for nf-core/tools version 3.0.0
79d1535
@nf-core-bot
Template update for nf-core/tools version 3.0.1
56e023f
@nf-core-bot
Template update for nf-core/tools version 3.0.2
69969cf
@LilyAnderssonLee
resolve the conflicts
226abd9
@LilyAnderssonLee
remove max_cpu from test.config
ff4d28f
@LilyAnderssonLee
update schema wit new release
f3ef6aa
@LilyAnderssonLee
add exists:true to the sechma to check the file path
5e90741
@LilyAnderssonLee
change db_path format back to the original value path in schema_database
a9af810
@LilyAnderssonLee
update the type of run_accession into string and integer
9e20ff1
@LilyAnderssonLee @jfy133
Update CITATIONS.md
88c9f46 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee @jfy133
Update conf/modules.config
2900ae2 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee
address comments from James
b0c1154
@LilyAnderssonLee @jfy133
Update nextflow.config
340b0af 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee
Add Lili as co-author
05b743f
@jfy133
Fix CI to run each test separately
fb38fb7
@LilyAnderssonLee @jfy133
Update main.nf
353188d 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@LilyAnderssonLee @jfy133
Update .nf-core.yml
f7c6176 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@nf-core-bot
[automated] Fix code linting
dbabb5d
@jfy133
Fix mOTUs if/else statemetn
fe84cc3
@LilyAnderssonLee
update configs and database schema
00067f5
@LilyAnderssonLee
Merge pull request #545 from nf-core/nf-core-template-merge-3.0.2
e34437b 
Important! Template update for nf-core/tools v3.0.2
@jfy133
Add darkmode version of metromap
8262e0a
@jfy133
Merge pull request #548 from nf-core/darkmode-diagram
93aa499 
Add darkmode version of metromap
@jfy133
Fix darkmode diagram
6c6cd8c
@Midnighter
refactor: prepare the additional prefixes input
2e6f37d 
The KrakenUniq module has a breaking change requiring a further input.
@Midnighter
chore: update krakenuniq/preloadedkrakenuniq
a1a8289
@Midnighter
fix: create always unique prefix
c0311a1
@Midnighter
fix: make prefix unique across PE and SE
30fc22a 
In the rare case that there are two samples with the same identifier and
run accession, one being single-end and the other paired-end, this
change makes the prefix and thus the KrakenUniq output filenames unique.
@jfy133
Update CHANGELOG.md
163d600
@jfy133
Merge pull request #549 from nf-core/darkmode-diagram
b2cac44 
Add darkmode diagram
sofstam and others added 30 commits January 9, 2025 14:17
@sofstam
Test new fix
6843bdf
@sofstam
Merge pull request #566 from sofstam/download_pipeline_fix
b4e9985 
Test fix for downloading
@jfy133
Use profile variable instead of hardcoding docker
6be6184
@jfy133
Merge pull request #567 from nf-core/fix-release-tests-for-condasingu…
c16ea83 
…larity

Use profile variable instead of hardcoding docker
@jfy133
Update CHANGELOG.md
320f6f2
@sofstam
Post-release bump version
26e610c
@sofstam
Update CHANGELOG.md
4f49fde
@sofstam
Prettier
2dea5b1
@sofstam
Merge branch 'bump_version_1.3.0' of https://github.com/nf-core/taxpr…
575ef87 
…ofiler into bump_version_1.3.0
@nf-core-bot
[automated] Fix code linting
7f5a785
@sofstam
Merge pull request #568 from nf-core/bump_version_1.3.0
071bcfb 
Post release bump version
@nf-core-bot
Template update for nf-core/tools version 3.1.2
64dcb04
@sofstam
Merge branch 'dev' into nf-core-template-merge-3.1.2
898866f
@sofstam
Update nextflow.config
ac960d4 
Fix is a template change, see nf-core/tools#3416
If your pipeline is affected by this error I think it should be fine to manually apply this patch.
@sofstam @jfy133
Update nextflow.config
a33a73f 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam
Update zenodo
f2226be
@sofstam
Update nextflow.config
3d54880
@jfy133
Update README.md
8b62db7
@jfy133
Apply suggestions from code review
b8a42de
@sofstam
Merge pull request #569 from nf-core/nf-core-template-merge-3.1.2
34c5079 
Important! Template update for nf-core/tools v3.1.2
@nf-core-bot
Template update for nf-core/tools version 3.2.0
622585a
@sofstam
Merge branch 'dev' into nf-core-template-merge-3.2.0
b524cb0
@jfy133
Merge pull request #571 from nf-core/nf-core-template-merge-3.2.0
f11fd27 
Important! Template update for nf-core/tools v3.2.0
@jfy133
Improve docs for taxpasta related flags
22380d6
@jfy133
Merge pull request #573 from nf-core/better-docs
7415c81 
Better docs for taxpasta related flags
@jfy133
Update CHANGELOG.md
ec1ac99
@jfy133
Merge pull request #575 from nf-core/changelog-for-docschagnes
c3a6b58 
Changelog for for #573
@mashehu
Fix keyword in nextflow_schema.json
4484e71
@mashehu
update changelog
612a94c
@mashehu
Merge pull request #578 from nf-core/fix-schema-keyword
24933cc 
Fix keyword in nextflow_schema.json
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6 participants
@LilyAnderssonLee @jfy133 @nf-core-bot @Midnighter @sofstam @mashehu