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feat: add maftools output #297

Merged
merged 60 commits into from
Aug 26, 2024
Merged

feat: add maftools output #297

merged 60 commits into from
Aug 26, 2024

Commits on Apr 18, 2024

  1. feat: add rules to generate maftools input files

    @dlaehnemann
    dlaehnemann committed Apr 18, 2024
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  2. request maftools input files in common.smk

    @dlaehnemann
    dlaehnemann committed Apr 18, 2024
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  3. include maftools activate option in default config.yaml 

    keep it set to false, so users have to actively turn it on
    @dlaehnemann
    dlaehnemann committed Apr 18, 2024
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  4. add maftools activation option to all testing config.yaml files, acti… 

    …vate in config-simple
    @dlaehnemann
    dlaehnemann committed Apr 18, 2024
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  5. add wildcard into maftools input file generation rules

    @dlaehnemann
    dlaehnemann committed Apr 18, 2024
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  6. fix missing quote and snakefmt

    @dlaehnemann
    dlaehnemann committed Apr 18, 2024
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Commits on Apr 24, 2024

  1. rename results folder for maftools to maftools

    @dlaehnemann
    dlaehnemann committed Apr 24, 2024
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  2. actually include maftools.smk in Snakefile

    @dlaehnemann
    dlaehnemann committed Apr 24, 2024
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  3. fix: remove module reference not needed after integration into workflow

    @dlaehnemann
    dlaehnemann committed Apr 24, 2024
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  4. fix: add forgotten conda environment def for vcf2maf

    @dlaehnemann
    dlaehnemann committed Apr 24, 2024
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  5. fix: path to newly included env

    @dlaehnemann
    dlaehnemann committed Apr 24, 2024
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Commits on May 28, 2024

  1. feat: make freebayes configurable via config.params.freebayes.extra

    @dlaehnemann
    dlaehnemann committed May 28, 2024
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Commits on Jun 3, 2024

  1. fix typo: extra " in config.yaml

    @dlaehnemann
    dlaehnemann committed Jun 3, 2024
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Commits on Jun 10, 2024

  1. Merge branch 'master' into feat/add-maftools-output

    @dlaehnemann
    dlaehnemann committed Jun 10, 2024
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Commits on Jun 17, 2024

  1. perf: switch to latest datavzrd wrapper to profit from recent perform… 

    …ance improvement
    @dlaehnemann
    dlaehnemann committed Jun 17, 2024
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Commits on Aug 19, 2024

  1. feat: refactor get_vembrane_config to allow re-use of plain FORMAT an… 

    …d INFO (and ANN) field names for vcf2maf conversion
    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  2. fix: levels if f and format in append_items() calls

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  3. chore: snakefmt workflow/rules/common.smk

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  4. fix: remove superfluous params: section 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @dlaehnemann @johanneskoester
    dlaehnemann and johanneskoester committed Aug 19, 2024
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  5. fix: address requeste refactoring from amftools to maf

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  6. fix: address update on main branch

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  7. Merge branch 'master' into feat/add-maftools-output

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  8. chore: manually follow snakefmt, as versions seem to diverge

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  9. fix: pass along the input

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  10. fix: search and replace didn't go into .test/ folder...

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  11. fix: properly pass on wildcards variable to get fusion info fields

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  12. fix: further maftools to maf refactoring

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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  13. fix: actually get_annotation_fields_for_tables()

    @dlaehnemann
    dlaehnemann committed Aug 19, 2024
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Commits on Aug 22, 2024

  1. fix: make re-inserting vaf columns in the right place more robust, si… 

    …mplify syntax
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  2. fix: typo

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  3. fix: ensure stable sort order, previously a lot was implicit

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  4. fix: typo, also sort ANN fields alphabetically where they are listed

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  5. fix: properly name fields (by type) for sort_order

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  6. fix: do not fail during column sorting, when certain columns not in c… 

    …olumns_dict
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  7. fix: it was no typo after all...

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  8. fix: add ANN['Gene'] field to sort_order, to keep it (needed internal… 

    …ly in split-call-tables.py)
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  9. fix: add fields to end of sort_order, that are used internally downst… 

    …ream, but not displayed in report
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  10. chore: snakefmt

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  11. fix: make all of the field getting functions work as function under t… 

    …he `params:` directive
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  12. fix: make alias selection tumor and alias selection for maf work via … 

    …config
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  13. fix: catch vcf2maf warnings, if tumor or normal alias is wrong; we wa… 

    …nt users to see and fix this
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  14. chore: also mention maf: tumor_alias and normal_alias in default conf… 

    …ig/config.yaml
    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  15. chore: address review comment

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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  16. chore: snakefmt

    @dlaehnemann
    dlaehnemann committed Aug 22, 2024
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Commits on Aug 23, 2024

  1. perf: update datavzrd version

    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  2. fix: make maf: introduction in config.yaml backwards compatible by us… 

    …ing lookup functions with defaults for all the fields
    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  3. fix: try providing False as default for vcf_normal_alias lookup in vc… 

    …f2maf
    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  4. fix: also test case where only a tumor_alias is specified for maf: … 

    …in `config.yaml`
    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  5. chore: remove maf: entry from all .test/ config.yaml files where … 

    …it is `activate: false`, except for one case (to test that syntax, as well)
    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  6. docs: indicate that maf output and plots are optional

    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  7. chore: remove superfluous whitespace

    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  8. fix: config-target-regions test samples.tsv and tumor_alias specifica… 

    …tion
    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  9. fix: vcf2maf normal_alias lookup syntax

    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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  10. fix: do not error on vcf2maf warning about NORMAL sample, as this is … 

    …the default expected `--vcf-normal-id` that is checked for, even if the optional `--normal-id` is not specified
    @dlaehnemann
    dlaehnemann committed Aug 23, 2024
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Commits on Aug 26, 2024

  1. fix: only elevate genotype column warnings of vcf2maf to errors

    @dlaehnemann
    dlaehnemann committed Aug 26, 2024
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  2. fix: bring back INFO['EVENT'] for proper breakend representation if… 

    … we need this

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @dlaehnemann @johanneskoester
    dlaehnemann and johanneskoester committed Aug 26, 2024
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  3. chore: refactor maf config from tumor_alias to primary_alias and norm… 

    …al_alias to control_alias, to make it clear that maf format and plotting can be used more generally
    @dlaehnemann
    dlaehnemann committed Aug 26, 2024
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  4. chore: remove some code redundancy

    @dlaehnemann
    dlaehnemann committed Aug 26, 2024
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  5. docs: make it clearer why we do the sorting in get_vembrane_config

    @dlaehnemann
    dlaehnemann committed Aug 26, 2024
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  6. chore: snakefmt

    @dlaehnemann
    dlaehnemann committed Aug 26, 2024
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