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Release v0.1.0 draft #8

Merged
merged 72 commits into from
Mar 5, 2025
Merged

Release v0.1.0 draft #8

merged 72 commits into from
Mar 5, 2025

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adamrtalbot
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Draft PR for release v0.1.0

Includes:

  • Update to latest nf-core template (v2.14.1)
  • Major refactor of code to simplify pipeline
  • Selective running of RNA or DNA pipelines via input parameters and samplesheet
  • Selective indexing of genome via input
  • Simplified workflow for higher throughput

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/dragen 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).
  • 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).

adamrtalbot and others added 30 commits May 3, 2024 11:04
@adamrtalbot
Template update for nf-core/tools version 2.13.1
30edead
@adamrtalbot
Template re-fixed?
f3cd395
@adamrtalbot
Resolve all the TEMPLATE stuff
1a558b0
@adamrtalbot
Opt-in for FASTQC and MultiQC instead of opt-out
317f5f8
@adamrtalbot
Re-add CHANGELOG details
0b76afa
@adamrtalbot
Revert configuration for modules
229e9f2
@adamrtalbot
Expand stubs to include echoing the Dragen CLI
e534b0c
@adamrtalbot
Optional index building based on input params
508ec36
@adamrtalbot
Merge pull request #3 from seqeralabs/TEMPLATE
0ba9671 
Template update for nf-core/tools version 2.13.1
@adamrtalbot
Remove additional variable
4706f66
@adamrtalbot
Complete optional indexing step
6778b76
@adamrtalbot
Update docs and improve consistency
9f7b22f
@adamrtalbot @maxulysse
Apply suggestions from code review
c597665 
Co-authored-by: Maxime U Garcia <[email protected]>
@adamrtalbot
Merge pull request #4 from seqeralabs/optional_build_indexes
697b8a9 
Optional build indexes step
@adamrtalbot
Adds optional sample type, which will run DNA or RNA pipeline only ba…
16af879 
…sed on input parameters
@adamrtalbot
Create single 'DRAGEN' workflow
19d4535 
Changes:
- Moves DRAGEN processes into single workflow
- Just INDEX and DRAGEN, everything else is done via args
- Moves FASTQC and MULTIQC into separate larger workflow
- Reuses workflow for RNA and DNA
@adamrtalbot
Use branching to selectively run RNA or DNA pipeline
00568c7
@adamrtalbot
Add FASTQC files to MultiQC inputs
55da40b
@adamrtalbot
Finish up some stuff
60a60a1
@adamrtalbot
Handle multiple FASTQ files per sample better
bf5a250
@adamrtalbot
DRAGEN process handles a wider variety of inputs correctly
6e49bbd
@adamrtalbot
Remove transcript quantification because we need transcript models fo…
69802ca 
…r this to work
@adamrtalbot
Update docs
3119bda
@adamrtalbot
Code alignment
505001c
@adamrtalbot
Merge pull request #5 from seqeralabs/optional_sample_type
873d5ab 
Optional sample type
@adamrtalbot
Miscellaneous fixes for dev
3fb2f01
@adamrtalbot
Update main.nf
dec7c14
@adamrtalbot
Merge pull request #6 from seqeralabs/misc_fixes
709460e 
Miscellaneous fixes for dev
@adamrtalbot
Use '?' instead of glob to handle individual FASTQ files better
dccb152
@adamrtalbot
Merge pull request #7 from seqeralabs/handle_single_fastq_files_better
d2f279b 
Use '?' instead of glob to handle individual FASTQ files better
adamrtalbot and others added 24 commits January 13, 2025 14:01
@adamrtalbot
.nf-core.yml output current dir
a403fc3
@adamrtalbot
Template update for nf-core/tools version 3.1.2.dev0
c8d9ce5
@adamrtalbot
Merge branch 'TEMPLATE' into template_update
7db4521
@adamrtalbot
linting fixes
41af558
@adamrtalbot
fix for samplesheet parsing
9188754
@adamrtalbot
fix some channel handling and versions
9493695
@adamrtalbot @maxulysse
Apply suggestions from code review
4d29a62 
Co-authored-by: Maxime U Garcia <[email protected]>
@adamrtalbot
bump resource requirements for Dragen process
62097ae
@adamrtalbot
Increase minimum resource limits for test
ec2b2b7
@adamrtalbot @maxulysse
Update nextflow.config
60a0993 
Co-authored-by: Maxime U Garcia <[email protected]>
@adamrtalbot
pr response
002ee3d
@adamrtalbot
Revert CHANGELOG
6998a4a
@adamrtalbot
Template update for nf-core/tools version 3.1.2.dev0
233bdb4
@adamrtalbot
Merge branch 'TEMPLATE' into template_update
cd62eef
@adamrtalbot
Revert CHANGELOG
06695e8
@adamrtalbot
Template update for nf-core/tools version 3.1.2.dev0
a4a7d65
@adamrtalbot
Merge branch 'TEMPLATE' into template_update
c0c603e
@adamrtalbot
update CHANGELOG
023c9ce
@adamrtalbot @maxulysse
dragen to nf-dragen
9ad5dd2 
The repo is called 'nf-dragen' so all changes must reflect this.

Co-authored-by: Maxime U Garcia <[email protected]>
@adamrtalbot
revert CHANGELOG.md
8f6af35
@adamrtalbot @maxulysse
Update main.nf
8126772 
Co-authored-by: Maxime U Garcia <[email protected]>
@adamrtalbot
CHANGELOG
9971bfb
@adamrtalbot
Merge pull request #10 from seqeralabs/template_update
7585fb9 
Template update to v3.1.1
@adamrtalbot
Revert license to MPL
80e4c09
@adamrtalbot adamrtalbot mentioned this pull request Jan 17, 2025
Merged
@adamrtalbot adamrtalbot merged commit 91d23c1 into master Mar 5, 2025
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@pditommaso pditommaso pditommaso left review comments

@maxulysse maxulysse maxulysse approved these changes

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@adamrtalbot @pditommaso @maxulysse