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chore: develop to master #387

Merged
merged 55 commits into from
Jan 26, 2024
Merged

chore: develop to master #387

merged 55 commits into from
Jan 26, 2024

Commits on Nov 29, 2023

  1. feat: new outputfile structure based on sample

    @jonca79
    jonca79 committed Nov 29, 2023
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Commits on Dec 6, 2023

  1. feat: add amino acid change to coverage_and_mutations

    @jonca79
    jonca79 committed Dec 6, 2023
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  2. fix: bugfix

    @jonca79
    jonca79 committed Dec 6, 2023
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Commits on Dec 8, 2023

  1. feat: updated hydra-genetics version

    @jonca79
    jonca79 committed Dec 8, 2023
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Commits on Dec 12, 2023

  1. fix: corrected input variables for hotspot_report.smk

    @jonca79
    jonca79 committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. fix: corrected input variables for hotspot_report.py

    @jonca79
    jonca79 committed Dec 13, 2023
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  2. fix: corrected input file for hotspot_report.smk

    @jonca79
    jonca79 committed Dec 13, 2023
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  3. feat: update to latest common container

    @jonca79
    jonca79 committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. fix: remove unused time consuming step in fusioncatcher

    @jonca79
    jonca79 authored Dec 14, 2023
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Commits on Dec 19, 2023

  1. fix: remove newline after purity in cnvkit_call command

    @jonca79
    jonca79 authored Dec 19, 2023
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  2. fix: update hydra-genetics to v1.10.1

    @jonca79
    jonca79 committed Dec 19, 2023
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  3. fix: input file bugfix

    @jonca79
    jonca79 committed Dec 19, 2023
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Commits on Dec 20, 2023

  1. fix: updated to bugfixed common container

    @jonca79
    jonca79 committed Dec 20, 2023
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Commits on Dec 21, 2023

  1. feat: decrease germline support needed to improve cnv visualization o… 

    …f deletions
    @jonca79
    jonca79 authored Dec 21, 2023
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  2. feat: decrease support needed for germline SNVs

    @jonca79
    jonca79 authored Dec 21, 2023
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  3. feat: restructured rna fusion report for improved interpretation

    @jonca79
    jonca79 committed Dec 21, 2023
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  4. fix: bugfixes

    @jonca79
    jonca79 committed Dec 21, 2023
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Commits on Dec 27, 2023

  1. fix: bugfix

    @jonca79
    jonca79 committed Dec 27, 2023
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  2. fix: reverse sorting and add chr to fusioncatcher

    @jonca79
    jonca79 committed Dec 27, 2023
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Commits on Jan 10, 2024

  1. fix: remove extra header columns

    @jonca79
    jonca79 committed Jan 10, 2024
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Commits on Jan 12, 2024

  1. fix: housekeeping dict

    @jonca79
    jonca79 authored Jan 12, 2024
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  2. feat: added dedup coverage

    @jonca79
    jonca79 committed Jan 12, 2024
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  3. test: pycodestyle

    @jonca79
    jonca79 committed Jan 12, 2024
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  4. test: fix breaking pulp version

    @jonca79
    jonca79 committed Jan 12, 2024
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  5. test: Update requirements.txt

    @jonca79
    jonca79 authored Jan 12, 2024
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Commits on Jan 16, 2024

  1. fix: changed sorting and bugfixes

    @jonca79
    jonca79 committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. feat: added umi vcf filters

    @jonca79
    jonca79 committed Jan 17, 2024
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  2. fix: pulp version

    @jonca79
    jonca79 authored Jan 17, 2024
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Commits on Jan 19, 2024

  1. Merge pull request #382 from genomic-medicine-sweden/speed_up_fusionc… 

    …atcher

fix: remove unused time consuming step in fusioncatcher
    @jonca79
    jonca79 authored Jan 19, 2024
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  2. Merge pull request #383 from genomic-medicine-sweden/rm_purity_newline 

    fix: remove newline after purity in cnvkit_call command
    @jonca79
    jonca79 authored Jan 19, 2024
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  3. Merge pull request #384 from genomic-medicine-sweden/CNV_BAF 

    feat: decrease germline support needed to improve cnv visualization o…
    @jonca79
    jonca79 authored Jan 19, 2024
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  4. Merge branch 'develop' into umi_filter

    @jonca79
    jonca79 authored Jan 19, 2024
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  5. Merge pull request #386 from genomic-medicine-sweden/umi_filter 

    feat: added umi vcf filters
    @jonca79
    jonca79 authored Jan 19, 2024
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  6. Merge branch 'develop' into rna_report

    @jonca79
    jonca79 authored Jan 19, 2024
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  7. Merge pull request #385 from genomic-medicine-sweden/rna_report 

    feat: restructured rna fusion report for improved interpretation
    @jonca79
    jonca79 authored Jan 19, 2024
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  8. fix: delete extra file

    @jonca79
    jonca79 authored Jan 19, 2024
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  9. Merge pull request #377 from genomic-medicine-sweden/output_per_sample 

    feat: new outputfile structure based on sample
    @jonca79
    jonca79 authored Jan 19, 2024
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  10. fix: corrected results path for soft-filtered umi vcf

    @jonca79
    jonca79 authored Jan 19, 2024
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  11. Merge pull request #381 from genomic-medicine-sweden/fix_coverage_and… 

    …_mutations

feat: add amino acid change to coverage_and_mutations
    @jonca79
    jonca79 authored Jan 19, 2024
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  12. Merge pull request #388 from genomic-medicine-sweden/fix_umi_output 

    fix: corrected results path for soft-filtered umi vcf
    @jonca79
    jonca79 authored Jan 19, 2024
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Commits on Jan 22, 2024

  1. fix: remove extra sample folder in output

    @jonca79
    jonca79 authored Jan 22, 2024
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  2. Merge pull request #390 from genomic-medicine-sweden/output_folder 

    fix: remove extra sample folder in output
    @jonca79
    jonca79 authored Jan 22, 2024
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  3. feat: update reports module to 0.3.1 (#389)

    @maehler
    maehler authored Jan 22, 2024
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Commits on Jan 25, 2024

  1. fix: added missing double mutations to report

    @jonca79
    jonca79 authored Jan 25, 2024
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  2. Merge pull request #392 from genomic-medicine-sweden/missing_double_m… 

    …utations

fix: added missing double mutations to report
    @jonca79
    jonca79 authored Jan 25, 2024
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  3. feat: update Jenkins main test

    @jonca79
    jonca79 authored Jan 25, 2024
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  4. fix: update jenkins start scripts

    @jonca79
    jonca79 authored Jan 25, 2024
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  5. fix: update profile with mounted home

    @jonca79
    jonca79 authored Jan 25, 2024
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  6. fix: update profile with mounted home

    @jonca79
    jonca79 authored Jan 25, 2024
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  7. fix: update profile with mounted home

    @jonca79
    jonca79 authored Jan 25, 2024
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  8. fix: update profile with mounted home

    @jonca79
    jonca79 authored Jan 25, 2024
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Commits on Jan 26, 2024

  1. fix: updated jenkins output for develop

    @jonca79
    jonca79 authored Jan 26, 2024
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  2. fix: corrected filepath for rna in develop

    @jonca79
    jonca79 authored Jan 26, 2024
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  3. fix: removed spaces in jenkins test develop

    @jonca79
    jonca79 authored Jan 26, 2024
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  4. Merge pull request #393 from genomic-medicine-sweden/update_jenkins 

    feat: update Jenkins main test
    @jonca79
    jonca79 authored Jan 26, 2024
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