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Candidate release 3.2.0 #1057

Merged
merged 561 commits into from
Jun 5, 2023
Merged

Candidate release 3.2.0 #1057

merged 561 commits into from
Jun 5, 2023
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Mar 2, 2023

  1. Merge pull request #954 from maxulysse/annotation_hg19 

    Fix missing annotation keys for vep/snpeff
    @maxulysse
    maxulysse committed Mar 2, 2023
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  2. add failsafe with join()

    @maxulysse
    maxulysse committed Mar 2, 2023
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Mar 2, 2023
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  4. expand to all join operators

    @maxulysse
    maxulysse committed Mar 2, 2023
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  5. update nf-core subworkflows

    @maxulysse
    maxulysse committed Mar 2, 2023
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  6. code polish

    @maxulysse
    maxulysse committed Mar 2, 2023
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  7. update CHANGELOG

    @maxulysse
    maxulysse committed Mar 2, 2023
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  8. no failOnMismatch for this join

    @maxulysse
    maxulysse committed Mar 2, 2023
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  9. update md5sum

    @maxulysse
    maxulysse committed Mar 2, 2023
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  10. no failOnDuplicate for this one

    @maxulysse
    maxulysse committed Mar 2, 2023
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  11. no failOnMismatch for this one

    @maxulysse
    maxulysse committed Mar 2, 2023
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  12. fix map

    @maxulysse
    maxulysse committed Mar 2, 2023
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  13. Merge pull request #957 from maxulysse/mutect2 

    Add failsafe options for Nextflow join operator
    @maxulysse
    maxulysse committed Mar 2, 2023
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Commits on Mar 15, 2023

  1. update paths

    @FriederikeHanssen
    FriederikeHanssen committed Mar 15, 2023
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  2. Merge pull request #965 from FriederikeHanssen/new_paths 

    update paths
    @ewels
    ewels committed Mar 15, 2023
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Commits on Mar 16, 2023

  1. add outdir_cache + update annotation docs for cache

    @maxulysse
    maxulysse committed Mar 16, 2023
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  2. Apply suggestions from code review 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @maxulysse @FriederikeHanssen
    maxulysse and FriederikeHanssen committed Mar 16, 2023
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  3. fix annotation cache test with conda

    @maxulysse
    maxulysse committed Mar 16, 2023
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  4. Apply suggestions from code review

    @maxulysse
    maxulysse committed Mar 16, 2023
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  5. Merge pull request #967 from maxulysse/annotation_cache_docs 

    ADD: Annotation cache usage docs
    @maxulysse
    maxulysse committed Mar 16, 2023
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Commits on Mar 17, 2023

  1. Merge branch 'dev' into ubam

    @maxulysse
    maxulysse committed Mar 17, 2023
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  2. update all modules

    @maxulysse
    maxulysse committed Mar 17, 2023
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Commits on Mar 18, 2023

  1. Don't mutate channel elements in-place

    @robsyme
    robsyme committed Mar 18, 2023
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Commits on Mar 20, 2023

  1. Changelog update

    @robsyme
    robsyme committed Mar 20, 2023
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  2. Merge pull request #971 from nf-core/sort-fix 

    Don't mutate channel elements in-place
    @maxulysse
    maxulysse committed Mar 20, 2023
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Commits on Mar 28, 2023

  1. Validate that sample/patient does not contain space and add test

    @matrulda
    matrulda committed Mar 28, 2023
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  2. Added how to generate ASCAT reference files for exome/targeted sequen… 

    …cing
    ameynert committed Mar 28, 2023
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  3. Fixed link formatting

    ameynert committed Mar 28, 2023
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  4. Add validation_checks tag to spaces test 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
    @matrulda @maxulysse
    matrulda and maxulysse committed Mar 28, 2023
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  5. Add new test to github actions workflow

    @matrulda
    matrulda committed Mar 28, 2023
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  6. Tab delimited output rather than underscore for loci files

    ameynert committed Mar 28, 2023
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  7. Merge pull request #978 from matrulda/issue-950_samplesheet_validatio… 

    …n_no_spaces

Issue 950: samplesheet validation - no spaces in sample or patient names
    @matrulda
    matrulda committed Mar 28, 2023
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  8. Use 'chr' prefix for loci and alleles

    ameynert committed Mar 28, 2023
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  9. Prettier linting

    @ameynert
    ameynert committed Mar 28, 2023
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  10. Merge pull request #1 from nf-core/dev 

    Merge from dev into forked dev
    ameynert committed Mar 28, 2023
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  11. #981

    ameynert committed Mar 28, 2023
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  12. Added Alison Meynert to contributors

    ameynert committed Mar 28, 2023
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Commits on Mar 29, 2023

  1. Clarified that ASCAT runs out of the box on WGS data

    ameynert committed Mar 29, 2023
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  2. Merge pull request #981 from ameynert/dev 

    ASCAT exome/targeted sequencing resource file generation
    ameynert committed Mar 29, 2023
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  3. Remove exit statements

    @FriederikeHanssen
    FriederikeHanssen committed Mar 29, 2023
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  4. Update changelog

    @FriederikeHanssen
    FriederikeHanssen committed Mar 29, 2023
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  5. don't lint since we are ahead of template

    @FriederikeHanssen
    FriederikeHanssen committed Mar 29, 2023
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Commits on Mar 30, 2023

  1. address reviews, remove nextflow.warn, replace with log

    @FriederikeHanssen
    FriederikeHanssen committed Mar 30, 2023
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  2. import nextflow

    @FriederikeHanssen
    FriederikeHanssen committed Mar 30, 2023
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Commits on Mar 31, 2023

  1. ADD: Cache correctly identifies when it needs to be updated

    @maxulysse
    maxulysse committed Mar 31, 2023
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  2. update changelog

    @maxulysse
    maxulysse committed Mar 31, 2023
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  3. Apply suggestions from code review 

    We don't need to `import nextflow.Nextflow` inside Nextflow scripts because the methods are already in scope
    @robsyme
    robsyme committed Mar 31, 2023
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  4. Merge pull request #982 from FriederikeHanssen/issue_805 

    Remove exit statements
    @FriederikeHanssen
    FriederikeHanssen committed Mar 31, 2023
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  5. Merge branch 'dev' into cache_hash

    @maxulysse
    maxulysse committed Mar 31, 2023
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  6. Merge pull request #985 from maxulysse/cache_hash 

    ADD: Cache correctly identifies when it needs to be updated
    @maxulysse
    maxulysse committed Mar 31, 2023
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Commits on Apr 5, 2023

  1. updated ascat module for reproducibility

    @SusiJo
    SusiJo committed Apr 5, 2023
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  2. update changelog

    @SusiJo
    SusiJo committed Apr 5, 2023
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  3. update changelog again

    @SusiJo
    SusiJo committed Apr 5, 2023
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  4. Merge pull request #988 from SusiJo/ascat_seed 

    Updated ascat for reproducibility
    @SusiJo
    SusiJo committed Apr 5, 2023
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Commits on Apr 11, 2023

  1. Merge branch 'dev' into gatk_update

    @maxulysse
    maxulysse committed Apr 11, 2023
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Commits on Apr 13, 2023

  1. Update manta to not use --exome flag for all interval files

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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  2. Remove interval parallelization

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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  3. update comments

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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  4. update changelog

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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  5. fix indent

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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  6. update checksums

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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  7. handle no intervals

    @FriederikeHanssen
    FriederikeHanssen committed Apr 13, 2023
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Commits on Apr 14, 2023

  1. update checksums

    @FriederikeHanssen
    FriederikeHanssen committed Apr 14, 2023
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  2. apply suggestions from review

    @FriederikeHanssen
    FriederikeHanssen committed Apr 14, 2023
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  3. Update subworkflows/local/bam_variant_calling_germline_manta/main.nf 

    Co-authored-by: Maxime U Garcia <maxime.garcia@scilifelab.se>
    @FriederikeHanssen @maxulysse
    FriederikeHanssen and maxulysse committed Apr 14, 2023
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  4. updating modules

    @maxulysse
    maxulysse committed Apr 14, 2023
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  5. Merge pull request #998 from FriederikeHanssen/issue_952 

    Issue 952
    @maxulysse
    maxulysse committed Apr 14, 2023
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Commits on Apr 25, 2023

  1. add INDEX creation

    @maxulysse
    maxulysse committed Apr 25, 2023
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  2. fix channels

    @maxulysse
    maxulysse committed Apr 25, 2023
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  3. typo

    @maxulysse
    maxulysse committed Apr 25, 2023
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  4. one liner

    @maxulysse
    maxulysse committed Apr 25, 2023
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  5. mode modules update

    @maxulysse
    maxulysse committed Apr 25, 2023
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  6. update CHANGELOG

    @maxulysse
    maxulysse committed Apr 25, 2023
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  7. Merge branch 'dev' into ubam

    @maxulysse
    maxulysse committed Apr 25, 2023
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  8. patch dragmap/hashtable

    @maxulysse
    maxulysse committed Apr 25, 2023
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  9. add ASCAT to updated tools

    @maxulysse
    maxulysse committed Apr 25, 2023
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  10. Merge pull request #928 from maxulysse/ubam 

    No need for BAI when using uBAM
    @maxulysse
    maxulysse committed Apr 25, 2023
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  11. remove conda tests as they almost always fail

    @maxulysse
    maxulysse committed Apr 25, 2023
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Commits on Apr 26, 2023

  1. remove md5sum

    @maxulysse
    maxulysse committed Apr 26, 2023
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  2. update subworkflow

    @maxulysse
    maxulysse committed Apr 26, 2023
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  3. update unzip module

    @maxulysse
    maxulysse committed Apr 26, 2023
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  4. update bcftools

    @maxulysse
    maxulysse committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. update bcftools related md5sum

    @maxulysse
    maxulysse committed Apr 27, 2023
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  2. update paths for untar tests

    @maxulysse
    maxulysse committed Apr 27, 2023
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  3. Merge pull request #968 from maxulysse/gatk_update 

    CHORE: update all modules
    @maxulysse
    maxulysse committed Apr 27, 2023
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Commits on Apr 28, 2023

  1. update subworkflows with proper schema

    @maxulysse
    maxulysse committed Apr 28, 2023
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  2. Merge pull request #1009 from maxulysse/subworkflows_update 

    CHORES: update subworkflows
    @maxulysse
    maxulysse committed Apr 28, 2023
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  3. Template update for nf-core/tools version 2.8

    @nf-core-bot
    nf-core-bot committed Apr 28, 2023
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Commits on May 3, 2023

  1. update TEMPLATE

    @maxulysse
    maxulysse committed May 3, 2023
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  2. merge TEMPLATE with 2.8

    @maxulysse
    maxulysse committed May 3, 2023
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  3. Merge branch 'dev' into sync_2.8

    @maxulysse
    maxulysse committed May 3, 2023
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  4. Apply suggestions from code review

    @maxulysse
    maxulysse committed May 3, 2023
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  5. prettier

    @maxulysse
    maxulysse committed May 3, 2023
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  6. fix syntax + prettier

    @maxulysse
    maxulysse committed May 3, 2023
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  7. Merge pull request #1011 from maxulysse/sync_2.8 

    CHORES: update TEMPLATE with 2.8
    @maxulysse
    maxulysse committed May 3, 2023
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  8. spacing in warning/error messages + collect -> first

    @maxulysse
    maxulysse committed May 3, 2023
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Commits on May 5, 2023

  1. spacing

    @maxulysse
    maxulysse committed May 5, 2023
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  2. more info

    @maxulysse
    maxulysse committed May 5, 2023
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  3. update annotation usage

    @maxulysse
    maxulysse committed May 5, 2023
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  4. update docs

    @maxulysse
    maxulysse committed May 5, 2023
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  5. Merge pull request #1014 from maxulysse/annotation_genome_null 

    fix genome null with annotation
    @maxulysse
    maxulysse committed May 5, 2023
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Commits on May 6, 2023

  1. increase default value for nucleotides_per_second reducing number of … 

    …groups
    @FriederikeHanssen
    FriederikeHanssen committed May 6, 2023
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  2. Update changelog and tests

    @FriederikeHanssen
    FriederikeHanssen committed May 6, 2023
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  3. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed May 6, 2023
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  4. Update CHANGELOG.md

    @FriederikeHanssen
    FriederikeHanssen committed May 6, 2023
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  5. Adapt description for intervals parameter

    @FriederikeHanssen
    FriederikeHanssen committed May 6, 2023
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  6. Merge remote-tracking branch 'origin/reduce_interval_groups' into red… 

    …uce_interval_groups
    @FriederikeHanssen
    FriederikeHanssen committed May 6, 2023
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  7. Merge pull request #1015 from FriederikeHanssen/reduce_interval_groups 

    Reduce interval groups default for smaller storage consumption
    @FriederikeHanssen
    FriederikeHanssen committed May 6, 2023
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Commits on May 10, 2023

  1. remove unnecessary substractions

    @maxulysse
    maxulysse committed May 10, 2023
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Commits on May 11, 2023

  1. Set a default registry outside of profile scope

    @maxulysse
    maxulysse committed May 11, 2023
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  2. update CHANGELOG

    @maxulysse
    maxulysse committed May 11, 2023
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  3. Merge pull request #1019 from maxulysse/patch-registry 

    Set a default registry outside of profile scope
    @maxulysse
    maxulysse committed May 11, 2023
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Commits on May 14, 2023

  1. fix snps_resource_label and indels_resource_label

    @asp8200
    asp8200 committed May 14, 2023
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Commits on May 15, 2023

  1. Again trying to get mix operator working with known_indels_vqsr known… 

    …_snps_vqsr and dbsnp_vqsr
    @asp8200
    asp8200 committed May 15, 2023
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  2. Trying to make sure that dbsnp_vqsr known_indels_vqsr and known_snps_… 

    …vqsr are channels and not strings
    @asp8200
    asp8200 committed May 15, 2023
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  3. Fixing copy-paste mistake

    @asp8200
    asp8200 committed May 15, 2023
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Commits on May 16, 2023

  1. Updating changelog

    @asp8200
    asp8200 committed May 16, 2023
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  2. Merge pull request #1022 from asp8200/fix_variantrecalibrator 

    Fix input channels for variantrecalibrator
    @maxulysse
    maxulysse committed May 16, 2023
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Commits on May 17, 2023

  1. remove unnecessary key from the meta map

    @maxulysse
    maxulysse committed May 17, 2023
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  2. clean up meta map

    @maxulysse
    maxulysse committed May 17, 2023
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Commits on May 22, 2023

  1. Update pipeline overview

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  2. Revert nextflow.config

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  3. Slight change to format

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  4. CHANGELOG

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  5. CHANGELOG

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  6. Change wording of the pipeline summary...summary

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  7. Remove VCF filtering tools

    @adamrtalbot
    adamrtalbot committed May 22, 2023
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  8. Merge pull request #1031 from adamrtalbot/update_pipeline_summary_may_23 

    Update pipeline overview
    @maxulysse
    maxulysse committed May 22, 2023
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Commits on May 23, 2023

  1. update all modules for correct registry usage

    @maxulysse
    maxulysse committed May 23, 2023
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  2. update CHANGELOG

    @maxulysse
    maxulysse committed May 23, 2023
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  3. Merge branch 'dev' into refactor

    @maxulysse
    maxulysse committed May 23, 2023
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  4. update CHANGELOG

    @maxulysse
    maxulysse committed May 23, 2023
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  5. patch dragmap/hashtable

    @maxulysse
    maxulysse committed May 23, 2023
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  6. Merge pull request #1012 from maxulysse/refactor 

    refactoring
    @maxulysse
    maxulysse committed May 23, 2023
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  7. update some subworkflows

    @maxulysse
    maxulysse committed May 23, 2023
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  8. Merge branch 'dev' into update_modules_registry

    @maxulysse
    maxulysse committed May 23, 2023
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  9. fix -profile test

    @maxulysse
    maxulysse committed May 23, 2023
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  10. fix deepvariant

    @maxulysse
    maxulysse committed May 23, 2023
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  11. fix manta germline subworkflow

    @maxulysse
    maxulysse committed May 23, 2023
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  12. fix bam_convert_samtools subworkflow

    @maxulysse
    maxulysse committed May 23, 2023
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  13. fix haplotypecaller subworkflow

    @maxulysse
    maxulysse committed May 23, 2023
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  14. remove true in fastp command when trimming

    @maxulysse
    maxulysse committed May 23, 2023
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  15. fix registry for local modules

    @maxulysse
    maxulysse committed May 23, 2023
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Commits on May 24, 2023

  1. fix gatk4_md_spark

    @maxulysse
    maxulysse committed May 24, 2023
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  2. fix deepvariant subworkflow + update md5sum in tests

    @maxulysse
    maxulysse committed May 24, 2023
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  3. fix cram_merge_index_samtools

    @maxulysse
    maxulysse committed May 24, 2023
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  4. fix several subworfklows

    @maxulysse
    maxulysse committed May 24, 2023
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  5. fix joint_germline subworkflow

    @maxulysse
    maxulysse committed May 24, 2023
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  6. fix mutect2 subworkflows

    @maxulysse
    maxulysse committed May 24, 2023
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  7. use older version of fastp

    @maxulysse
    maxulysse committed May 24, 2023
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  8. Merge pull request #1032 from maxulysse/update_modules_registry 

    update all modules for correct registry usage
    @maxulysse
    maxulysse committed May 24, 2023
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Commits on May 25, 2023

  1. remove concatenate_vcfs tests with singularity

    @maxulysse
    maxulysse committed May 25, 2023
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  2. update CHANGELOG

    @maxulysse
    maxulysse committed May 25, 2023
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  3. Merge pull request #1039 from maxulysse/concatenate_singularity 

    Remove concatenate_vcfs tests with singularity
    @FriederikeHanssen
    FriederikeHanssen committed May 25, 2023
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  4. Merge branch 'dev' into maxulysse-patch-1

    @maxulysse
    maxulysse committed May 25, 2023
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  5. update CHANGELOG

    @maxulysse
    maxulysse committed May 25, 2023
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  6. update

    @maxulysse
    maxulysse committed May 25, 2023
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  7. remove error strategy for manta/strelka

    @maxulysse
    maxulysse committed May 25, 2023
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  8. update CHANGELOG

    @maxulysse
    maxulysse committed May 25, 2023
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  9. fix dict channel issue when using --dict

    @maxulysse
    maxulysse committed May 25, 2023
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  10. Merge pull request #1040 from maxulysse/fix_dict_channel 

    FIX: dict channel issue when using params.dict
    @maxulysse
    maxulysse committed May 25, 2023
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  11. ADD: vep_custom_args

    @maxulysse
    maxulysse committed May 25, 2023
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  12. fix type

    @maxulysse
    maxulysse committed May 25, 2023
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  13. use proper default value

    @maxulysse
    maxulysse committed May 25, 2023
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  14. Update nextflow_schema.json 

    Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @maxulysse @FriederikeHanssen
    maxulysse and FriederikeHanssen committed May 25, 2023
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  15. Update nextflow_schema.json

    @maxulysse
    maxulysse committed May 25, 2023
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  16. Update nextflow_schema.json

    @maxulysse
    maxulysse committed May 25, 2023
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  17. Update nextflow_schema.json

    @maxulysse
    maxulysse committed May 25, 2023
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Commits on May 26, 2023

  1. Merge pull request #1041 from maxulysse/custom_vep_args 

    ADD: new vep_custom_args
    @maxulysse
    maxulysse committed May 26, 2023
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  2. fix typos

    @maxulysse
    maxulysse committed May 26, 2023
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  3. Merge branch 'dev' into tests_yml

    @maxulysse
    maxulysse committed May 26, 2023
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  4. update CHANGELOG

    @maxulysse
    maxulysse committed May 26, 2023
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  5. Merge pull request #1043 from maxulysse/tests_yml 

    FIX: typos
    @maxulysse
    maxulysse committed May 26, 2023
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  6. Adds public_aws_ecr profile for using ECR hosted images. 

    Additions:
 - Adds public_aws_ecr profile which:
    - Sets the default registry to public.ecr.aws
    - Replaces all processes that aren't available on ECR with full URI
    @adamrtalbot
    adamrtalbot committed May 26, 2023
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  7. CHANGELOG

    @adamrtalbot
    adamrtalbot committed May 26, 2023
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  8. fixup

    @adamrtalbot
    adamrtalbot committed May 26, 2023
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  9. Merge pull request #1045 from adamrtalbot/public_aws_ecr_profile 

    Adds public_aws_ecr profile for using ECR hosted images.
    @adamrtalbot
    adamrtalbot committed May 26, 2023
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Commits on May 29, 2023

  1. don't check for tumor/normal and tools distribution if annotation is … 

    …done
    @FriederikeHanssen
    FriederikeHanssen committed May 29, 2023
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  2. switch tumor and normal counting to be in sync with samplesheet speci… 

    …fication
    @FriederikeHanssen
    FriederikeHanssen committed May 29, 2023
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  3. bams should be bams and crams should be crams

    @FriederikeHanssen
    FriederikeHanssen committed May 29, 2023
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  4. changelog

    @FriederikeHanssen
    FriederikeHanssen committed May 29, 2023
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  5. tis a function

    @FriederikeHanssen
    FriederikeHanssen committed May 29, 2023
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  6. Merge pull request #1048 from FriederikeHanssen/input_val 

    Input validation fixes
    @FriederikeHanssen
    FriederikeHanssen committed May 29, 2023
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Commits on May 30, 2023

  1. Disable GATK filters when joint calling

    @amizeranschi
    amizeranschi committed May 30, 2023
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  2. Update CHANGELOG.md

    @amizeranschi
    amizeranschi committed May 30, 2023
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Commits on May 31, 2023

  1. CHORES: update FASTP

    @maxulysse
    maxulysse committed May 31, 2023
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  2. remove diff file

    @maxulysse
    maxulysse committed May 31, 2023
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  3. update samtools/faidx

    @maxulysse
    maxulysse committed May 31, 2023
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  4. Apply suggestions from code review

    @maxulysse
    maxulysse committed May 31, 2023
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  5. Merge pull request #1051 from maxulysse/fastp 

    CHORES: modules update
    @maxulysse
    maxulysse committed May 31, 2023
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Commits on Jun 1, 2023

  1. Merge pull request #1050 from amizeranschi/amizeranschi-issue-1025 

    Disable GATK filters when joint calling
    @maxulysse
    maxulysse committed Jun 1, 2023
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  2. fix pattern for fasta file

    @maxulysse
    maxulysse committed Jun 1, 2023
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Jun 1, 2023
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  4. update CHANGELOG

    @maxulysse
    maxulysse committed Jun 1, 2023
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  5. bump version to 3.2.0

    @maxulysse
    maxulysse committed Jun 1, 2023
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  6. use biocontainer provided container

    @maxulysse
    maxulysse committed Jun 1, 2023
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  7. update CHANGELOG

    @maxulysse
    maxulysse committed Jun 1, 2023
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  8. Update conf/test/test_full.config

    @maxulysse
    maxulysse committed Jun 1, 2023
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  9. Merge pull request #1058 from maxulysse/registry_update 

    FIX: VCFTOOLS public ecr registry
    @maxulysse
    maxulysse committed Jun 1, 2023
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  10. Merge branch 'dev' into json_fix

    @maxulysse
    maxulysse committed Jun 1, 2023
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  11. Merge branch 'dev' into maxulysse-patch-1

    @maxulysse
    maxulysse committed Jun 1, 2023
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  12. update MANTA/STRELKA modules

    @maxulysse
    maxulysse committed Jun 1, 2023
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  13. Merge pull request #1056 from maxulysse/prepare_release 

    CHORES: bump to 3.2.0
    @maxulysse
    maxulysse committed Jun 1, 2023
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Commits on Jun 2, 2023

  1. Merge pull request #882 from nf-core/maxulysse-patch-1 

    remove exit strategy for MANTA/STRELKA
    @maxulysse
    maxulysse committed Jun 2, 2023
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  2. Merge pull request #1055 from nf-core/json_fix 

    FIX: pattern for fasta file
    @maxulysse
    maxulysse committed Jun 2, 2023
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  3. don't publish genomicsdb files

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  4. why, meta map, why?

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  5. more views

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  6. more views

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  7. use dump

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  8. use dump

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  9. backtrack [skip ci]

    @FriederikeHanssen
    FriederikeHanssen committed Jun 2, 2023
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  10. more printing [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  11. more printing [skip ci]

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  12. don't mess with metamap separation [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  13. turn of groupKey but keep meta [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  14. add ouput [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  15. fix automatic restart

    @maxulysse
    maxulysse committed Jun 2, 2023
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  16. update CHANGELOG

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  17. add ouput [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  18. Merge pull request #1062 from maxulysse/restart 

    FIX: automatic restart from step
    @maxulysse
    maxulysse committed Jun 2, 2023
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  19. maybe its the fasta [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  20. revertc changes [skip ci]

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  21. [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  22. clean up

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    FriederikeHanssen committed Jun 2, 2023
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  23. clean up

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    FriederikeHanssen committed Jun 2, 2023
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  24. clean up

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    FriederikeHanssen committed Jun 2, 2023
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  25. fix comment

    @maxulysse
    maxulysse committed Jun 2, 2023
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  26. FIX: join mismatch for annotation

    @maxulysse
    maxulysse committed Jun 2, 2023
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  27. update CHANGELOG

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    maxulysse committed Jun 2, 2023
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  28. clean up

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    FriederikeHanssen committed Jun 2, 2023
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  29. dumpchannel [skip ci]

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    FriederikeHanssen committed Jun 2, 2023
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  30. playaround with single interval

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  31. Merge pull request #1063 from maxulysse/mismatch_join 

    FIX: join duplication for manta/strelka annotation
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    FriederikeHanssen committed Jun 2, 2023
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  32. 0 and 1 are in fact not the same

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    FriederikeHanssen committed Jun 2, 2023
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  33. Update changelog

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    FriederikeHanssen committed Jun 2, 2023
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  34. Merge branch 'dev' into issue_1035

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  35. Apply suggestions from code review 

    Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @maxulysse @FriederikeHanssen
    maxulysse and FriederikeHanssen committed Jun 2, 2023
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  36. Apply suggestions from code review 

    Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @maxulysse @FriederikeHanssen
    maxulysse and FriederikeHanssen committed Jun 2, 2023
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  37. Update lib/WorkflowMain.groovy 

    Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @maxulysse @FriederikeHanssen
    maxulysse and FriederikeHanssen committed Jun 2, 2023
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  38. Update docs/usage.md

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  39. Merge pull request #1061 from FriederikeHanssen/issue_1035 

    don't publish genomicsdb files
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    maxulysse committed Jun 2, 2023
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Commits on Jun 5, 2023

  1. Apply suggestions from code review 

    Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @maxulysse @FriederikeHanssen
    maxulysse and FriederikeHanssen committed Jun 5, 2023
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  2. Apply suggestions from code review

    @maxulysse
    maxulysse committed Jun 5, 2023
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  3. remove Sarek version from images

    @maxulysse
    maxulysse committed Jun 5, 2023
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  4. update CHANGELOG

    @maxulysse
    maxulysse committed Jun 5, 2023
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  5. update CHANGELOG

    @maxulysse
    maxulysse committed Jun 5, 2023
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  6. fixoutput docs

    @FriederikeHanssen
    FriederikeHanssen committed Jun 5, 2023
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  7. Merge pull request #1070 from maxulysse/update_images 

    CHORES: remove version from pictures
    @FriederikeHanssen
    FriederikeHanssen committed Jun 5, 2023
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  8. Merge pull request #1071 from FriederikeHanssen/release_fixes 

    docs update
    @maxulysse
    maxulysse committed Jun 5, 2023
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