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chore: dev to main #55

Merged
merged 70 commits into from
Apr 18, 2024
Merged

chore: dev to main #55

merged 70 commits into from
Apr 18, 2024

Commits on Feb 15, 2024

  1. ci: update config files and create new marvin profiles

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  2. feat: add annotations to svdb merged vcf using svdb query of local SV… 

    … dbs
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Commits on Feb 16, 2024

  1. feat: use priority in svdb merge

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Commits on Feb 22, 2024

  1. feat: add gnomda af with vep 110

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  2. ci: update requirements

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  3. docs: update docs

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Commits on Feb 23, 2024

  1. refactor: change the name for trios in samples.tsv

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  2. Update output_list.json

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    padraicc authored Feb 23, 2024
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  3. fix error in output file name

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    padraicc committed Feb 23, 2024
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  4. fix error in output file name

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    padraicc authored Feb 23, 2024
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  5. Update output_list.json

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    padraicc authored Feb 23, 2024
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  6. Update output_list.json

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    padraicc authored Feb 23, 2024
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  7. Update Snakefile

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    padraicc authored Feb 23, 2024
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  8. ci: Update multiqc version

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    padraicc authored Feb 23, 2024
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  9. Update output_list.json

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    padraicc authored Feb 23, 2024
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  10. ci: update cnv_sv module

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    padraicc authored Feb 23, 2024
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  11. Update Snakefile

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    padraicc authored Feb 23, 2024
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  12. Update Snakefile

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    padraicc authored Feb 23, 2024
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Commits on Feb 24, 2024

  1. Use bcftools filter for soft filtering

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    padraicc authored Feb 24, 2024
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  2. Update config.yaml

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    padraicc authored Feb 24, 2024
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Commits on Mar 12, 2024

  1. feat: update the alignment module version

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  2. update output json

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  3. update config for compatability with new alignment module

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    padraicc committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. feat: use run_deepvariant script in updated snv_indels module

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  2. removed local sample files

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    padraicc committed Mar 13, 2024
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Commits on Mar 14, 2024

  1. ci: update compression module

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  2. ci: reduce bwa mem threads

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    padraicc committed Mar 14, 2024
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Commits on Mar 26, 2024

  1. ci: Update config.yaml

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    padraicc authored Mar 26, 2024
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  2. ci: Update resources.yaml

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    padraicc authored Mar 26, 2024
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Commits on Mar 27, 2024

  1. switch back to original trio id in samples.tsv

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    padraicc committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. ci: update parabricks for deepvariant v1.6

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  2. ci: add script to generate order and replacement files

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    padraicc committed Mar 28, 2024
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  3. ci: updaate cnv_sv module version

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    padraicc committed Mar 28, 2024
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  4. ci: remove old script

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    padraicc committed Mar 28, 2024
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  5. ci: update config

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    padraicc committed Mar 28, 2024
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Commits on Apr 9, 2024

  1. docs: start using rtd

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    padraicc committed Apr 9, 2024
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Commits on Apr 10, 2024

  1. docs: update docs

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    padraicc committed Apr 10, 2024
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  2. refactor: change rule to work with snakemale docs plugin

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    padraicc committed Apr 10, 2024
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Commits on Apr 13, 2024

  1. ci: Update config.schema.yaml

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    padraicc authored Apr 13, 2024
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  2. feat: improve handling of config validation

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    padraicc authored Apr 13, 2024
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  3. remove extra validation check

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    padraicc authored Apr 13, 2024
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  4. fix: update manta input names

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    padraicc authored Apr 13, 2024
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Commits on Apr 15, 2024

  1. remove unneeded rule order

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    padraicc authored Apr 15, 2024
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  2. feat: remove temp on peddy sex check file 

    Removing temp on the peddy sex check result is needed to stop 
a whole pipeline re-run being triggered when an error is encountered after it is deleted.
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  3. feat: add peddy html report to output_list.json

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    padraicc authored Apr 15, 2024
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Commits on Apr 16, 2024

  1. Merge branch 'develop' into novaseq_x_validation

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  2. docs: update mkdocs nav

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    padraicc committed Apr 16, 2024
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  3. style: fix style of rules and scripts

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    padraicc committed Apr 16, 2024
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  4. ci: update requirements

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    padraicc committed Apr 16, 2024
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  5. tests: update modules in test config

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  6. refactor: use named input for svdb merge

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  7. tests: update to python 3.9

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    padraicc committed Apr 16, 2024
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  8. style: snakefmt rules

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    padraicc committed Apr 16, 2024
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  9. tests: remove conda path from lint test

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    padraicc authored Apr 16, 2024
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  10. refactor: remove prints and rename rule

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    padraicc committed Apr 16, 2024
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  11. Merge branch 'novaseq_x_validation' of github.com:clinical-genomics-u… 

    …ppsala/poirot_rd_wgs into novaseq_x_validation
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  12. docs: update rulegraph

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    padraicc committed Apr 16, 2024
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  13. docs: update dag graph

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    padraicc committed Apr 16, 2024
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  14. chore: remove conda env files and old shell scripts

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    padraicc committed Apr 16, 2024
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  15. tests: create seperate dry run for CPU and GPU mode

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  16. tests: update dry-run test description

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  17. feat: use misc module for bgzip and tabix

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    padraicc committed Apr 16, 2024
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  18. style: snakefmt Snakefile

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    padraicc committed Apr 16, 2024
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  19. Update snakemake version in requirements.txt

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    padraicc authored Apr 16, 2024
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  20. chore: cleanup unnecessary files

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Commits on Apr 17, 2024

  1. docs: update REAME

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    padraicc committed Apr 17, 2024
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  2. docs: update dag image

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    padraicc committed Apr 17, 2024
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  3. docs: update README

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    padraicc committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. feat: update hydra-modules

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    padraicc committed Apr 18, 2024
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  2. Merge pull request #54 from clinical-genomics-uppsala/novaseq_x_valid… 

    …ation

ci: update config files and create new marvin profiles
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    padraicc authored Apr 18, 2024
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