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Remove docker command wrappers; CPSR refactor #193

Merged
merged 33 commits into from Jul 11, 2022
Merged

Remove docker command wrappers; CPSR refactor #193

merged 33 commits into from Jul 11, 2022

Commits on Jul 3, 2022

  1. pcgr_validate_input: no default output_dir

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    pdiakumis committed Jul 3, 2022
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  2. utils: remove docker references

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    pdiakumis committed Jul 3, 2022
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  3. utils: get loftee dir

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    pdiakumis committed Jul 3, 2022
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  4. cpsr_validate_input: no default output_dir

    @pdiakumis
    pdiakumis committed Jul 3, 2022
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  5. arg_checker: host_directories -> pcgr_paths

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    pdiakumis committed Jul 3, 2022
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  6. modularise cpsr funcs/vars

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    pdiakumis committed Jul 3, 2022
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  7. cpsr: modularise funcs/vars; remove docker wrappers

    @pdiakumis
    pdiakumis committed Jul 3, 2022
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  8. pcgr main: remove docker wrappers

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    pdiakumis committed Jul 3, 2022
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  9. cpsr.py: fix indentation

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    pdiakumis committed Jul 3, 2022
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  10. main.py: shorten maf help msg

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    pdiakumis committed Jul 3, 2022
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  11. Genomics England PanelApp -> GEP

    @pdiakumis
    pdiakumis committed Jul 3, 2022
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  12. cleanup help msg

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    pdiakumis committed Jul 3, 2022
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  13. remove trailing whitespace

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    pdiakumis committed Jul 3, 2022
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  14. refactor/align pcgr_validate_input

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    pdiakumis committed Jul 3, 2022
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  15. refactor utils; remove EBI vcf-validation; use debug in scripts

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    pdiakumis committed Jul 3, 2022
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  16. pcgr_summarise: fix indentation

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    pdiakumis committed Jul 3, 2022
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  17. pcgr_vcfanno: fix indentation

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    pdiakumis committed Jul 3, 2022
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  18. pcgr_vcfanno: add debug/logger

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    pdiakumis committed Jul 3, 2022
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Commits on Jul 4, 2022

  1. pcgr_summarise: use vars_no_csq for succinct logging

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    pdiakumis committed Jul 4, 2022
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  2. main.py: refactor debug/logging

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    pdiakumis committed Jul 4, 2022
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  3. cpsr: fix indentation

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    pdiakumis committed Jul 4, 2022
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  4. cpsr: logging

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    pdiakumis committed Jul 4, 2022
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Commits on Jul 5, 2022

  1. cpsr: support version checking

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    pdiakumis committed Jul 5, 2022
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  2. pcgr: log multiallelics in list

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    pdiakumis committed Jul 5, 2022
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  3. cpsr: log multiallelics in list; fix debug

    @pdiakumis
    pdiakumis committed Jul 5, 2022
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  4. pcgr/cpsr: remove --docker_uid, --no_docker options

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    pdiakumis committed Jul 5, 2022
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Commits on Jul 6, 2022

  1. log up to 100 of multiallelic/intergenic records

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    pdiakumis committed Jul 6, 2022
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Commits on Jul 7, 2022

  1. output TRUE/FALSE in log for "skip intergenic"

    @pdiakumis
    pdiakumis committed Jul 7, 2022
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  2. remove NEWS.md from pcgrr (using CHANGELOG instead)

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    pdiakumis committed Jul 7, 2022
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  3. use unzip_if_gzipped_cmd when simplifying and sorting input_vcf

    @pdiakumis
    pdiakumis committed Jul 7, 2022
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Commits on Jul 9, 2022

  1. fix ICGC-PCAWG rendering

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    pdiakumis committed Jul 9, 2022
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  2. fix vcf unzipping

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    pdiakumis committed Jul 9, 2022
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  3. fix

    @pdiakumis
    pdiakumis committed Jul 9, 2022
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