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Bouncy basenji pre-release PR #519

Merged
merged 135 commits into from
Sep 11, 2024
Merged

Bouncy basenji pre-release PR #519

merged 135 commits into from
Sep 11, 2024

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jfy133
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@jfy133 jfy133 commented Sep 4, 2024 •
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prep for bouncy release

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 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).

jfy133 and others added 30 commits November 9, 2023 19:57
@jfy133
Install module
a58388c
@jfy133
Merge pull request #416 from nf-core/dev
b25350c 
Sync with dev
@jfy133
Add get it working, add to tests, update docs/images/citations
69e0d09
@jfy133
Fix groovy semantic errors
2c24711
@jfy133
update gitignore to ignore nf-test
1a37251
@jfy133
Revert "update gitignore to ignore nf-test"
240634c 
This reverts commit 1a37251.
@jfy133
Fix nonpareil args across all tests
5e853b0
@jfy133
Add nonpareil
a050658
@jfy133
Minor linting
ff16394
@jfy133
Fix channel emission
46bf2b2
@jfy133
Fix module linting
c69b00e
@jfy133
Add nonpareil to valid MultiQC entries
a0d5821
@jfy133
Final linting
c1d12d9
@nf-core-bot
[automated] Fix linting with Prettier
88b8e1a
@jfy133 @LilyAnderssonLee
Apply suggestions from code review
40d1bfa 
Co-authored-by: Lili Andersson-Li <[email protected]>
@jfy133
Merge pull request #417 from nf-core/add-nonpareil
ffff2e6 
Add nonpareil
@jfy133
Merge branch 'dev' into bouncy-basenji
5ea76e8
@sofstam
Merge dev into bouncy-basenji
f4dd39b
@jfy133
Fix prettier
f00bd54
@jfy133
Remove merge marker
45dd3c9
@jfy133
Merge branch 'bouncy-basenji' into fix-merge-conflict
d9de044
@jfy133
Merge pull request #448 from nf-core/fix-merge-conflict
aa6d088 
Dev to bouncy-basenji
@LilyAnderssonLee
Merge dev into bouncy-basenji
c22f6e9
@LilyAnderssonLee
Merge pull request #455 from LilyAnderssonLee/bouncy-basenji
faf93e9 
Merge dev into bouncy-basenji
@LilyAnderssonLee
update the nanopore and fasta input channel
9373a96
@LilyAnderssonLee
Merge branch 'nf-core:master' into fix-validation
b0d2ad3
@LilyAnderssonLee
add fallback to download pipeline workflow
ff977f6
@LilyAnderssonLee
update nf-validation
b89aba6
@LilyAnderssonLee @jfy133
Update workflows/taxprofiler.nf
d0a58e2 
Co-authored-by: James A. Fellows Yates <[email protected]>
@LilyAnderssonLee
Update taxprofiler.nf
dabc253
LilyAnderssonLee and others added 25 commits September 4, 2024 11:05
@LilyAnderssonLee
Publish the ganon classify log file in the output
a90456d
@LilyAnderssonLee
update motus/profile
c4d5ed7
@LilyAnderssonLee
update modules, most changes happened in nf-test
81902b3
@LilyAnderssonLee
update utils_nextflow_pipeline and utils_nfcore_pipeline
d429463
@LilyAnderssonLee
Merge branch 'nf-core:master' into update_tools
8a42385
@LilyAnderssonLee
merge dev to the current branch
75efdb7
@LilyAnderssonLee
separate fasta into fasta_shrt and fasta_long
4e2b85f
@LilyAnderssonLee
Update changelog
2f3ea43
@LilyAnderssonLee
add nanoq is default option to the usage
bd66c35
@LilyAnderssonLee
unique check for fasta file names
4ef2579
@LilyAnderssonLee
state that the pipeline is built on nextflow to README.md
54cb683
@LilyAnderssonLee @sofstam
Update CHANGELOG.md
ef5db33 
Co-authored-by: Sofia Stamouli <[email protected]>
@LilyAnderssonLee
Update CHANGELOG.md
9a23069
@LilyAnderssonLee
update modules
df25a1b
@LilyAnderssonLee
Merge pull request #512 from genomic-medicine-sweden/update_tools
c6dfb84 
Update modules
@jfy133
Remove porechop_abi patch
8b5b635
@jfy133
Fix patches on PORECHOP modules
0774258
@jfy133
Fix formatting
8ea3e7c
@LilyAnderssonLee
fix pre-commit linting
b22bb1d
@jfy133
Merge pull request #522 from nf-core/remove-nanopore-patch
8949ad4 
Remove nanopore patch
@LilyAnderssonLee
replace output-lca into -m lca in ganon classify
af8bc72
@jfy133
Drop unnecesary ganon parameter (should come via db_params) and patte…
9500726 
…rn for classify to 2.0 valid,
@jfy133
Update output docs
5bc5716
@jfy133
Update parameter docs
8bf5833
@jfy133
Merge pull request #523 from nf-core/ganon-classy-lca
cc34d41 
correct parameter to use lca for multiple matches in ganon classify
@jfy133 jfy133 changed the title [DONOTMERGE] Bouncy basenji release Bouncy basenji pre-release PR Sep 11, 2024
LilyAnderssonLee
LilyAnderssonLee approved these changes Sep 11, 2024
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LGTM

@LilyAnderssonLee LilyAnderssonLee merged commit b63da73 into dev Sep 11, 2024
25 checks passed
@LilyAnderssonLee LilyAnderssonLee deleted the bouncy-basenji branch September 11, 2024 05:56
@jfy133 jfy133 restored the bouncy-basenji branch September 11, 2024 08:27
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@jfy133 @LilyAnderssonLee @nf-core-bot @sofstam