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Update ichorcna to v0.5.1 and nf-test #6079

Merged
merged 37 commits into from
Aug 23, 2024
Merged

Update ichorcna to v0.5.1 and nf-test #6079

merged 37 commits into from
Aug 23, 2024

Commits on Jan 23, 2023

  1. Module: ichorcna/run updated to v0.5.0 

    Changes:
 - ichorcna no longer has a CLI, so it has been updated to use native R
 - Some additional parameters have been added
 - Requires scStates option in nextflow.config or it crashes
    Adam Talbot committed Jan 23, 2023
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Commits on Jan 31, 2023

  1. Merge branch 'master' into ichorcna_run_update

    @adamrtalbot
    adamrtalbot authored Jan 31, 2023
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Commits on Feb 1, 2023

  1. ichorcna/run gc_wig not optional

    Adam Talbot committed Feb 1, 2023
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  2. ichorcna/run centromere put above other parameters as it is more impo… 

    …rtant
    Adam Talbot committed Feb 1, 2023
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  3. ichorcna correct test URLS

    Adam Talbot committed Feb 1, 2023
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  4. Merge branch 'master' into ichorcna_run_update

    Adam Talbot committed Feb 1, 2023
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Commits on Mar 7, 2023

  1. Merge branch 'master' into ichorcna_run_update

    @adamrtalbot
    adamrtalbot authored Mar 7, 2023
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  2. Merge branch 'master' into ichorcna_run_update

    @adamrtalbot
    adamrtalbot authored Mar 7, 2023
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  3. fix meta.yml and change the name to normal_background

    @adamrtalbot
    adamrtalbot committed Mar 7, 2023
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  4. Merge branch 'master' into ichorcna_run_update

    @adamrtalbot
    adamrtalbot authored Mar 7, 2023
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  5. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Mar 7, 2023
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Commits on Oct 2, 2023

  1. Merge branch 'master' into ichorcna_run_update

    @SPPearce
    SPPearce authored Oct 2, 2023
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Commits on Dec 6, 2023

  1. Merge branch 'master' into ichorcna_run_update

    @SPPearce
    SPPearce authored Dec 6, 2023
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  2. Update environment to 0.5.0

    @SPPearce
    SPPearce committed Dec 6, 2023
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  3. createpon test

    @SPPearce
    SPPearce committed Dec 6, 2023
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Commits on Aug 1, 2024

  1. Swap to nftest and test 0.5.1 docker

    @SPPearce
    SPPearce committed Aug 1, 2024
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  2. Merge remote-tracking branch 'origin/master' into ichorcna_run_update

    @SPPearce
    SPPearce committed Aug 1, 2024
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  3. Remove from tests

    @SPPearce
    SPPearce committed Aug 1, 2024
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  4. Reset test.yml

    @SPPearce
    SPPearce committed Aug 1, 2024
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  5. Merge branch 'master' into ichorcna_run_update

    @SPPearce
    SPPearce authored Aug 1, 2024
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  6. Update output channels and snapshot

    @SPPearce
    SPPearce committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. Update snap and meta

    @SPPearce
    SPPearce committed Aug 2, 2024
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  2. Merge branch 'master' into ichorcna_run_update

    @SPPearce
    SPPearce authored Aug 2, 2024
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Commits on Aug 3, 2024

  1. Update PoN

    @SPPearce
    SPPearce committed Aug 3, 2024
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Commits on Aug 5, 2024

  1. Merge branch 'master' into ichorcna_run_update

    @SPPearce
    SPPearce authored Aug 5, 2024
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Commits on Aug 6, 2024

  1. Add stub and additional asserts to PoN

    @SPPearce
    SPPearce committed Aug 6, 2024
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  2. change output directory of bclconvert & bcl2fastq (#6112) 

    * change output directory

* fix linting

* update snapshot

* update lane

* delete environment.yml
    @atrigila @SPPearce
    atrigila authored and SPPearce committed Aug 6, 2024
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  3. Updated test data paths batch 11 (#6085) 

    * Updated test data paths

* Added --depthcutoff for freyja/boot
    @GallVp @SPPearce
    GallVp authored and SPPearce committed Aug 6, 2024
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  4. Updated test data paths batch 17 (#6103) 

    Updated paths
    @GallVp @SPPearce
    GallVp authored and SPPearce committed Aug 6, 2024
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  5. Updated test data paths batch 19 (#6105) 

    * Updated paths

* Updated shapshot for liftlong
    @GallVp @SPPearce
    GallVp authored and SPPearce committed Aug 6, 2024
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  6. chore(deps): update actions/setup-java digest to 6a0805f (#6114) 

    Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
    @renovate @SPPearce
    renovate[bot] authored and SPPearce committed Aug 6, 2024
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  7. Updated test data paths batch 18 (#6104) 

    * Updated test data paths batch 18

* Fixed instrain version in conda file

* Fixed instrain version in conda file

* Removed db content md5 from snapshot to pass conda test

* Added samtools to instrain env

* Updated snapshot
    @GallVp @SPPearce
    GallVp authored and SPPearce committed Aug 6, 2024
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  8. Bump chromap version to chromap modules (#6113) 

    * Bump chromap version to chromap/index

* Bump chromap version to chromap/chromap

* Use nft-bam as suggested in review

* Change how prefix for output index is set to be modifiable
    @JoseEspinosa @SPPearce
    JoseEspinosa authored and SPPearce committed Aug 6, 2024
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  9. Add stub, nf-tests and bump version 3.5.5 to deeptools modules (#6109) 

    * Update deeptools/plotheatmap

* Update deeptols/multibamsummary

* Update plotpca

* Update deeptools/computematrix

* Update deeptools/bamcoverage

* Remove comment

* Update deeptools/plotcorrelation

* Fix c/p error

* Update deeptools/plotfingerprint

* Update nf-core/deeptools

* Add deeptools/plotprofile snapshot

* Simplify tests and fix some issues

* Make lint happy

* Make lint happy

* Reverting plotheatmap meta.yml

* Fix input declaration in meta yaml

* Fix multibamsummary tags

* Fix value type in meta.yml

* Remove pytest for deeptools modules

* Add missing tags in compound test runs

* Fix tyop

* Apply review suggestions

* Update modules/nf-core/deeptools/bamcoverage/main.nf

Co-authored-by: Simon Pearce <[email protected]>

* Update snapshot for deeptools/bamcoverage after applying review suggestion

* Change how prefix for output index is set to be modifiable

* Revert last commit (wrong branch) :P

---------

Co-authored-by: Simon Pearce <[email protected]>
    @JoseEspinosa @SPPearce
    JoseEspinosa and SPPearce committed Aug 6, 2024
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  10. Bracken bug fix (#6119) 

    * Allow for construction of standard database

* Update meta to include standard database

* Fix bug for passing in -l with ext.args

* Full correction

* Update test snapshots

* Add test corresponding to the genus issue

* Revert "Allow for construction of standard database"

This reverts commit 71b800e.

* Revert "Update meta to include standard database"

This reverts commit 1d48333.
    @egreenberg7 @SPPearce
    egreenberg7 authored and SPPearce committed Aug 6, 2024
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  11. Add nf-test to krakentools/combinekreports (#6120) 

    add nf-test to krakentools/combinekreports
    @LilyAnderssonLee @SPPearce
    LilyAnderssonLee authored and SPPearce committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Merge branch 'master' into ichorcna_run_update

    @SPPearce
    SPPearce authored Aug 7, 2024
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