Code

from megafusion to vcf_collect#414

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Merged

rannick merged 55 commits intodevnf-core/rnafusion:devfrom megafusion_to_vcf_collectnf-core/rnafusion:megafusion_to_vcf_collectCopy head branch name to clipboardNov 20, 2023

+2,144-321

Commits

Commits on Sep 29, 2023

• from megafusion to vcf_collect

  rannick

  committed
  1ea68bc

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Commits on Oct 2, 2023

• start collecting more information with vcf_collect

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  committed
  da68e1d

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• Merge branch 'dev' into megafusion_to_vcf_collect

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  42679f7

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Commits on Oct 23, 2023

• Merge branch 'dev' into megafusion_to_vcf_collect

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  385b05a

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Commits on Oct 30, 2023

• add hgnc id and extra info for vcf file

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  committed
  41bd823

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• add hgnc id and extra info for vcf file

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  committed
  4ba9728

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• fix merging conflicts

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  committed
  cd2b4ee

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• fix channel i/o

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  committed
  b0c0f18

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• black

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  605280b

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• fix bug in channel i/o

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  committed
  36519af

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• fix bug in channel i/o

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  committed
  fd80774

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• add hgnc download to build_references workflow

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  committed
  3db4665

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• add hgnc download to build_references workflow

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  committed
  71b15d5

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• add meta info for hgnc

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  committed
  52bf004

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Commits on Oct 31, 2023

• update gtfparse containers

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  committed
  b07cee3

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• fix bug with param genome.s

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  committed
  bdb1a6e

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Commits on Nov 1, 2023

• add AGAT/CONVERTSPGFF2TSV to convert gtf to tsv

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  aa74611

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Commits on Nov 6, 2023

• Merge branch 'dev' into megafusion_to_vcf_collect

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  7a516b9

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• install agat/convertspgff2tsv from nf-core

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  committed
  cc4ec30

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• correct typo

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  0c3ffae

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• vcf_collect takes tsv_coding_effect channel instead of tsv

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  ba55fa3

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• remove empty entry

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  1b9c181

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• make optional gtf and coding effectsg

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  committed
  775444e

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• remove HGNC: from HGNC id column

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  4a38147

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• fix hgnc date timestamping

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  6f2a4ea

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• black

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  committed
  f4c0912

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Commits on Nov 7, 2023

• add support for case fusioninspector filters out a fusion from fusionreport

  rannick

  committed
  4337f4a

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• Merge branch 'dev' into megafusion_to_vcf_collect

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  3736e69

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Commits on Nov 8, 2023

• update changelog

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  be99aef

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• Merge branch 'dev' into megafusion_to_vcf_collect

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  3c1a8d5

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Commits on Nov 10, 2023

• Update bin/vcf_collect.py

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  fevac

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  1c109ff

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• Apply suggestions from code review

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Commits on Nov 13, 2023

• use fstrings

  rannick

  committed
  92a3dad

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• add info on GTF output file from fusioninspector

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  7a700f0

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• Merge branch 'dev' into megafusion_to_vcf_collect

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  00d12a2

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• black

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  committed
  22e4502

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• Merge branch 'megafusion_to_vcf_collect' of https://github.com/nf-core/rnafusion into megafusion_to_vcf_collect

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  committed
  a2b485f

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• fix header typer

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  committed
  e59823c

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• mend

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  committed
  afda8fd

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• Revert "mend"

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  f14bd90

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• revert to plain pandas container

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  committed
  55d95d1

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• sample should just be meta.id, add fusion_data in module for output name

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  committed
  6bc7351

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• remove quotes and flatten the pseudo list in annots

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  committed
  d559232

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• back to original container

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  committed
  d0a4bf2

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• revert to pandas

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  b468942

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Commits on Nov 14, 2023

• apply fixes

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  committed
  960db4c

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Commits on Nov 15, 2023

• Merge branch 'dev' into megafusion_to_vcf_collect

  rannick

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  3084301

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• compress vcf output

  rannick

  committed
  852c6ac

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• Merge branch 'megafusion_to_vcf_collect' of https://github.com/nf-core/rnafusion into megafusion_to_vcf_collect

  rannick

  committed
  7801cab

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• black

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  committed
  9643ed8

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• modules updatge

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  committed
  bb703dd

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• move compression out of vcf_collect

  rannick

  committed
  ef9f57a

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• fix ,/;

  rannick

  committed
  f33a5e9

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Commits on Nov 16, 2023

• fix values display vcf

  rannick

  committed
  a8b0743

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Commits on Nov 17, 2023

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

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  committed
  acf64a1

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