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741 add nanopore support #830

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wants to merge 16 commits into from
Closed

741 add nanopore support #830

wants to merge 16 commits into from

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samuell
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@samuell samuell commented Jan 30, 2025

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/ampliseq 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).

d4straub and others added 16 commits April 3, 2024 12:24
@d4straub
Merge pull request nf-core#725 from nf-core/dev
717abb8 
Release 2.9.0
@d4straub
Merge pull request nf-core#755 from nf-core/dev
3f40a1b 
Release 2.10.0
@d4straub
Merge pull request nf-core#771 from nf-core/dev
0473e15 
Release 2.11.0
@d4straub
Release 2.12.0
8f139ce 
Release 2.12.0
@erikrikarddaniel @samuell
Add sbdi-gtdb R09-RS220
1fa79ca
@samuell
Adapt base config for local laptop
068c55b
@samuell
Add Emu to main AmpliSeq workflow
c12d522
@samuell
Add changes for Emu to nextflow.config
ffe4f8b
@samuell
Add changes for Emu to modules.config
731caef
@samuell
Add changes for Emu to nextflow_schema.json
7f8fe12
@samuell
Add changes for Emu to utils_nfcore_ampliseq_pipeline/main.nf
d112422
@samuell
Add the Emu module createdy by Frans Wallin (@fwa93)
1084628
@samuell
Turn off stuff not relevant when analyzing Nanopore data
bdb8782
@samuell
Remove hard-coded paths
fcade0a
@samuell
Add missing reads param in schema
bef1dbb
@samuell
Run nf-core pipelines schema build to format schema file
aa66a94
@nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@samuell samuell closed this Jan 30, 2025
@samuell samuell deleted the 741-add-nanopore-support branch January 30, 2025 18:57
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4 participants
@samuell @nf-core-bot @d4straub @erikrikarddaniel