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from megafusion to vcf_collect #414

Merged
merged 55 commits into from
Nov 20, 2023
Merged

from megafusion to vcf_collect #414

merged 55 commits into from
Nov 20, 2023

Commits on Sep 29, 2023

  1. from megafusion to vcf_collect

    @rannick
    rannick committed Sep 29, 2023
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Commits on Oct 2, 2023

  1. start collecting more information with vcf_collect

    @rannick
    rannick committed Oct 2, 2023
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  2. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Oct 2, 2023
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Commits on Oct 23, 2023

  1. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Oct 23, 2023
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Commits on Oct 30, 2023

  1. add hgnc id and extra info for vcf file

    @rannick
    rannick committed Oct 30, 2023
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  2. add hgnc id and extra info for vcf file

    @rannick
    rannick committed Oct 30, 2023
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  3. fix merging conflicts

    @rannick
    rannick committed Oct 30, 2023
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  4. fix channel i/o

    @rannick
    rannick committed Oct 30, 2023
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  5. black

    @rannick
    rannick committed Oct 30, 2023
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  6. fix bug in channel i/o

    @rannick
    rannick committed Oct 30, 2023
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  7. fix bug in channel i/o

    @rannick
    rannick committed Oct 30, 2023
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  8. add hgnc download to build_references workflow

    @rannick
    rannick committed Oct 30, 2023
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  9. add hgnc download to build_references workflow

    @rannick
    rannick committed Oct 30, 2023
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  10. add meta info for hgnc

    @rannick
    rannick committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. update gtfparse containers

    @rannick
    rannick committed Oct 31, 2023
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  2. fix bug with param genome.s

    @rannick
    rannick committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. add AGAT/CONVERTSPGFF2TSV to convert gtf to tsv

    @rannick
    rannick committed Nov 1, 2023
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Commits on Nov 6, 2023

  1. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Nov 6, 2023
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  2. install agat/convertspgff2tsv from nf-core

    @rannick
    rannick committed Nov 6, 2023
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  3. correct typo

    @rannick
    rannick committed Nov 6, 2023
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  4. vcf_collect takes tsv_coding_effect channel instead of tsv

    @rannick
    rannick committed Nov 6, 2023
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  5. remove empty entry

    @rannick
    rannick committed Nov 6, 2023
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  6. make optional gtf and coding effectsg

    @rannick
    rannick committed Nov 6, 2023
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  7. remove HGNC: from HGNC id column

    @rannick
    rannick committed Nov 6, 2023
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  8. fix hgnc date timestamping

    @rannick
    rannick committed Nov 6, 2023
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  9. black

    @rannick
    rannick committed Nov 6, 2023
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Commits on Nov 7, 2023

  1. add support for case fusioninspector filters out a fusion from fusion… 

    …report
    @rannick
    rannick committed Nov 7, 2023
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  2. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Nov 7, 2023
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Commits on Nov 8, 2023

  1. update changelog

    @rannick
    rannick committed Nov 8, 2023
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  2. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Nov 8, 2023
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Commits on Nov 10, 2023

  1. Update bin/vcf_collect.py 

    Co-authored-by: Eva C <[email protected]>
    @rannick @fevac
    rannick and fevac authored Nov 10, 2023
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  2. Apply suggestions from code review 

    Co-authored-by: Eva C <[email protected]>
    @rannick @fevac
    rannick and fevac authored Nov 10, 2023
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Commits on Nov 13, 2023

  1. use fstrings

    @rannick
    rannick committed Nov 13, 2023
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  2. add info on GTF output file from fusioninspector

    @rannick
    rannick committed Nov 13, 2023
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  3. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Nov 13, 2023
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  4. black

    @rannick
    rannick committed Nov 13, 2023
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  5. Merge branch 'megafusion_to_vcf_collect' of https://github.com/nf-cor… 

    …e/rnafusion into megafusion_to_vcf_collect
    @rannick
    rannick committed Nov 13, 2023
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  6. fix header typer

    @rannick
    rannick committed Nov 13, 2023
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  7. mend

    @rannick
    rannick committed Nov 13, 2023
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  8. Revert "mend" 

    This reverts commit afda8fd.
    @rannick
    rannick committed Nov 13, 2023
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  9. revert to plain pandas container

    @rannick
    rannick committed Nov 13, 2023
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  10. sample should just be meta.id, add fusion_data in module for output name

    @rannick
    rannick committed Nov 13, 2023
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  11. remove quotes and flatten the pseudo list in annots

    @rannick
    rannick committed Nov 13, 2023
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  12. back to original container

    @rannick
    rannick committed Nov 13, 2023
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  13. revert to pandas

    @rannick
    rannick committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. apply fixes

    @rannick
    rannick committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. Merge branch 'dev' into megafusion_to_vcf_collect

    @rannick
    rannick authored Nov 15, 2023
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  2. compress vcf output

    @rannick
    rannick committed Nov 15, 2023
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  3. Merge branch 'megafusion_to_vcf_collect' of https://github.com/nf-cor… 

    …e/rnafusion into megafusion_to_vcf_collect
    @rannick
    rannick committed Nov 15, 2023
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  4. black

    @rannick
    rannick committed Nov 15, 2023
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  5. modules updatge

    @rannick
    rannick committed Nov 15, 2023
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  6. move compression out of vcf_collect

    @rannick
    rannick committed Nov 15, 2023
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  7. fix ,/;

    @rannick
    rannick committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. fix values display vcf

    @rannick
    rannick committed Nov 16, 2023
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Commits on Nov 17, 2023

  1. add hgnc id for fusionreport-only entries in vcf and add bug fix

    @rannick
    rannick committed Nov 17, 2023
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