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First release :) #1

Merged
merged 28 commits into from
Dec 16, 2024
Merged

First release :) #1

merged 28 commits into from
Dec 16, 2024

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famosab
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@famosab famosab commented Dec 10, 2024 •
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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
  • 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).

famosab added 27 commits December 4, 2024 15:20
@famosab
feat: add modules
dbe6d85
@famosab
feat: add docker image
e2a10f9
@famosab
fix: swap to wave containers
43675e0
@famosab
feat: update schema and config
5b669e9
@famosab
feat: add modules to workflow
4e605ba
@famosab
fix: usage of vcf2mat
717346b
@famosab
fix: remove .view and add more comments explaining the code
533805c
@famosab
feat: add gvcf to vcf conversion
61fb027
@famosab
feat: add GATK iGenomes
dae598e
@famosab
feat: add tabix
d3518a9
@famosab
update docs
1af1f01
@famosab
update input schema
17fe77b
@famosab
update sbwf
ddc017d
@famosab
update schemas
7bf1719
@famosab
add pipeline tests
577b7d2
@famosab
feat: add correct tests
0d4b2ee
@famosab
change access to index bool
2ada853
@famosab
prettier to hopefullly fix linting?
12542ec
@famosab
fix indentation
66b1103
@famosab
add env to local module
621ca11
@famosab
fix linting for first version
9813674
@famosab
add nf-test and ignore external configs
e8aeda6
@famosab
wip on nf-test
6d0e881
@famosab
finalize tests
f8eb870
@famosab
Template update for nf-core/tools version 3.0.2
e35329f
@famosab
Template update for nf-core/tools version 3.1.0
363ab73
@famosab
Merge branch 'TEMPLATE' into dev
cc93eb3
@famosab
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famosab commented Dec 16, 2024

This will be called
Curie Purpureal

https://www.codenamegenerator.com/ - Units of Measurement / Color Terms

famosab
famosab commented Dec 16, 2024
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@famosab famosab merged commit acf9ad5 into master Dec 16, 2024
16 of 20 checks passed
famosab added a commit that referenced this pull request Dec 17, 2024
@famosab
Fix/filenamecoll (#5)
4dc0279 
* First release :) (#1)

* feat: add modules

* feat: add docker image

* fix: swap to wave containers

* feat: update schema and config

* feat: add modules to workflow

* fix: usage of vcf2mat

* fix: remove .view and add more comments explaining the code

* feat: add gvcf to vcf conversion

* feat: add GATK iGenomes

* feat: add tabix

* update docs

* update input schema

* update sbwf

* update schemas

* add pipeline tests

* feat: add correct tests

* change access to index bool

* prettier to hopefullly fix linting?

* fix indentation

* add env to local module

* fix linting for first version

* add nf-test and ignore external configs

* wip on nf-test

* finalize tests

* Template update for nf-core/tools version 3.0.2

* Template update for nf-core/tools version 3.1.0

* Apply suggestions from code review

* Change famosab to qbic-pipelines after transfer (#2)

* Update README.md after transfer

* change famosab to qbic-pipelines

* update main

* fix: filename collision by using filebasename and include modules config again

* fix: update snaps

* prettier
famosab added a commit that referenced this pull request Jan 8, 2025
@famosab @d4straub
Release 1.1.0 (#11)
e93735a 
* feat: add modules

* feat: add docker image

* fix: swap to wave containers

* feat: update schema and config

* feat: add modules to workflow

* fix: usage of vcf2mat

* fix: remove .view and add more comments explaining the code

* feat: add gvcf to vcf conversion

* feat: add GATK iGenomes

* feat: add tabix

* update docs

* update input schema

* update sbwf

* update schemas

* add pipeline tests

* feat: add correct tests

* change access to index bool

* prettier to hopefullly fix linting?

* fix indentation

* add env to local module

* fix linting for first version

* add nf-test and ignore external configs

* wip on nf-test

* finalize tests

* Template update for nf-core/tools version 3.0.2

* Template update for nf-core/tools version 3.1.0

* Apply suggestions from code review

* fix: filename collision by using different subsets of the filename (#4)

* Fix/filenamecoll (#5)

* First release :) (#1)

* feat: add modules

* feat: add docker image

* fix: swap to wave containers

* feat: update schema and config

* feat: add modules to workflow

* fix: usage of vcf2mat

* fix: remove .view and add more comments explaining the code

* feat: add gvcf to vcf conversion

* feat: add GATK iGenomes

* feat: add tabix

* update docs

* update input schema

* update sbwf

* update schemas

* add pipeline tests

* feat: add correct tests

* change access to index bool

* prettier to hopefullly fix linting?

* fix indentation

* add env to local module

* fix linting for first version

* add nf-test and ignore external configs

* wip on nf-test

* finalize tests

* Template update for nf-core/tools version 3.0.2

* Template update for nf-core/tools version 3.1.0

* Apply suggestions from code review

* Change famosab to qbic-pipelines after transfer (#2)

* Update README.md after transfer

* change famosab to qbic-pipelines

* update main

* fix: filename collision by using filebasename and include modules config again

* fix: update snaps

* prettier

* add sample names to columns and restructure (#7)

* add sample names and restructure

* add new param

* prettier

* expand docs

* remove weird param

* bump-version to dev

* prettier

* tests

* add concatenation of same saples with same label (#8)

* add concatenation of same saples with same label

* update changelog and docs

* maybe we need to switch to a subway map soon

* try other ci file

* try other ci file

* fix name

* remove ci from linting

* update pipeline level tests

* ignore modules

* add nft-vcf

* update ci and snaps

* modify

* revert

* prepare release 1.1.0 (#10)

* prepare release

* version correction

* prettier

* fix schema

* remove dev

Co-authored-by: Daniel Straub <[email protected]>

* add forgotten explanations to output

* prettier

---------

Co-authored-by: Daniel Straub <[email protected]>
famosab added a commit that referenced this pull request Jan 8, 2025
@famosab @d4straub
Back to dev (#13)
6a3c6dc 
* Release 1.1.0 (#11)

* feat: add modules

* feat: add docker image

* fix: swap to wave containers

* feat: update schema and config

* feat: add modules to workflow

* fix: usage of vcf2mat

* fix: remove .view and add more comments explaining the code

* feat: add gvcf to vcf conversion

* feat: add GATK iGenomes

* feat: add tabix

* update docs

* update input schema

* update sbwf

* update schemas

* add pipeline tests

* feat: add correct tests

* change access to index bool

* prettier to hopefullly fix linting?

* fix indentation

* add env to local module

* fix linting for first version

* add nf-test and ignore external configs

* wip on nf-test

* finalize tests

* Template update for nf-core/tools version 3.0.2

* Template update for nf-core/tools version 3.1.0

* Apply suggestions from code review

* fix: filename collision by using different subsets of the filename (#4)

* Fix/filenamecoll (#5)

* First release :) (#1)

* feat: add modules

* feat: add docker image

* fix: swap to wave containers

* feat: update schema and config

* feat: add modules to workflow

* fix: usage of vcf2mat

* fix: remove .view and add more comments explaining the code

* feat: add gvcf to vcf conversion

* feat: add GATK iGenomes

* feat: add tabix

* update docs

* update input schema

* update sbwf

* update schemas

* add pipeline tests

* feat: add correct tests

* change access to index bool

* prettier to hopefullly fix linting?

* fix indentation

* add env to local module

* fix linting for first version

* add nf-test and ignore external configs

* wip on nf-test

* finalize tests

* Template update for nf-core/tools version 3.0.2

* Template update for nf-core/tools version 3.1.0

* Apply suggestions from code review

* Change famosab to qbic-pipelines after transfer (#2)

* Update README.md after transfer

* change famosab to qbic-pipelines

* update main

* fix: filename collision by using filebasename and include modules config again

* fix: update snaps

* prettier

* add sample names to columns and restructure (#7)

* add sample names and restructure

* add new param

* prettier

* expand docs

* remove weird param

* bump-version to dev

* prettier

* tests

* add concatenation of same saples with same label (#8)

* add concatenation of same saples with same label

* update changelog and docs

* maybe we need to switch to a subway map soon

* try other ci file

* try other ci file

* fix name

* remove ci from linting

* update pipeline level tests

* ignore modules

* add nft-vcf

* update ci and snaps

* modify

* revert

* prepare release 1.1.0 (#10)

* prepare release

* version correction

* prettier

* fix schema

* remove dev

Co-authored-by: Daniel Straub <[email protected]>

* add forgotten explanations to output

* prettier

---------

Co-authored-by: Daniel Straub <[email protected]>

* Update README.md with Zenodo DOI (#12)

---------

Co-authored-by: Daniel Straub <[email protected]>
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