Code

Enhancement/hg38 update#128

Code

Merged

anoronh4 merged 35 commits intodevelopmskcc/forte:developfrom enhancement/hg38_updatemskcc/forte:enhancement/hg38_updateCopy head branch name to clipboardJan 13, 2025

+4,306-384

Commits

Commits on Sep 20, 2024

• updating GRCh38 references

  

  Anne Marie Noronha

  committed
  d19f77a

  Copy full SHA for d19f77a

Commits on Sep 23, 2024

• fix gtf channel for GRCh38 mode

  anoronh4

  committed
  f8069a2

  Copy full SHA for f8069a2

• update star/genomegenerate

  anoronh4

  committed
  16dd74e

  Copy full SHA for 16dd74e

Commits on Sep 25, 2024

• adjustments to make GRCh38 run through

  anoronh4

  committed
  e30de97

  Copy full SHA for e30de97

• Merge branch 'develop' into enhancement/hg38_update

  anoronh4

  committed
  b97fea0

  Copy full SHA for b97fea0

• fix indentation

  anoronh4

  committed
  e206da4

  Copy full SHA for e206da4

Commits on Sep 26, 2024

• fix agfusion download command

  anoronh4

  committed
  fa7f511

  Copy full SHA for fa7f511

• clean up view operator

  anoronh4

  committed
  20379c7

  Copy full SHA for 20379c7

• fix fillout pytest

  anoronh4

  committed
  39744f7

  Copy full SHA for 39744f7

• change pfam reference to stagnant release

  anoronh4

  committed
  01b2981

  Copy full SHA for 01b2981

• add poison pill to reference channels

  anoronh4

  committed
  7325589

  Copy full SHA for 7325589

• update md5sum in test_profile test

  anoronh4

  committed
  c204119

  Copy full SHA for c204119

• update ensembl version to 112

  anoronh4

  committed
  7c5dc28

  Copy full SHA for 7c5dc28

• update CHANGELOG.md

  anoronh4

  committed
  d8e423f

  Copy full SHA for d8e423f

Commits on Oct 1, 2024

• change ensembl version to 111

  anoronh4

  committed
  4966057

  Copy full SHA for 4966057

• update AGFusion to [email protected]

  anoronh4

  committed
  3bbaecf

  Copy full SHA for 3bbaecf

• fix conflicts

  anoronh4

  committed
  3ea6c20

  Copy full SHA for 3ea6c20

• Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into enhancement/hg38_update

  anoronh4

  committed
  29f10aa

  Copy full SHA for 29f10aa

Commits on Oct 2, 2024

• add cpus in AGAT_SPADDINTRONS resources

  anoronh4

  committed
  cd06afc

  Copy full SHA for cd06afc

• fix indentation

  anoronh4

  committed
  3bfeb91

  Copy full SHA for 3bfeb91

• Set gene_id as gene_name for lncRNAs, remove NF transcripts from gene bed

  pintoa1-mskcc

  committed
  9147321

  Copy full SHA for 9147321

• Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into enhancement/hg38_update

  anoronh4

  committed
  6e09888

  Copy full SHA for 6e09888

• fix linting error, ensure no scientific notation in gene bed

  pintoa1-mskcc

  committed
  ad50743

  Copy full SHA for ad50743

• Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into enhancement/hg38_update

  pintoa1-mskcc

  committed
  db34bad

  Copy full SHA for db34bad

Commits on Oct 10, 2024

• remove deprecated arriba installation

  anoronh4

  committed
  95e737e

  Copy full SHA for 95e737e

• update to decoy fasta

  anoronh4

  committed
  3d97ab8

  Copy full SHA for 3d97ab8

• Merge branch 'develop' into enhancement/hg38_update

  pintoa1-mskcc

  authored
  32507d5

  Copy full SHA for 32507d5

• add storeDir directives for gunzip* and FASTAREMOVEPREFIX

  anoronh4

  committed
  7f8c7c0

  Copy full SHA for 7f8c7c0

• Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into enhancement/hg38_update

  anoronh4

  committed
  6fcb29c

  Copy full SHA for 6fcb29c

• change chromosome M to MT in fasta

  anoronh4

  committed
  709317a

  Copy full SHA for 709317a

Commits on Oct 11, 2024

• add idt_v2 baits for GRCh38 to reference config

  anoronh4

  committed
  a70828d

  Copy full SHA for a70828d

Commits on Nov 7, 2024

• edit genebed generation to function with v111 nomenclature

  pintoa1-mskcc

  committed
  612a80a

  Copy full SHA for 612a80a

• linting errors

  pintoa1-mskcc

  committed
  1e0d3f1

  Copy full SHA for 1e0d3f1

• line endings

  pintoa1-mskcc

  committed
  e105305

  Copy full SHA for e105305

Commits on Nov 13, 2024

• Modify generate gene bed to one script

  pintoa1-mskcc

  committed
  fb2f514

  Copy full SHA for fb2f514