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Enhancement/hg38 update #128

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Enhancement/hg38 update #128

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anoronh4
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@anoronh4 anoronh4 commented Sep 25, 2024 •
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Addresses #129

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the mskcc/forte branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@anoronh4 anoronh4 linked an issue Sep 25, 2024 that may be closed by this pull request
update for GRCh38 #129
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anoronh4 and others added 18 commits September 25, 2024 21:39
@anoronh4
fix agfusion download command
fa7f511
@anoronh4
clean up view operator
20379c7
@anoronh4
fix fillout pytest
39744f7
@anoronh4
change pfam reference to stagnant release
01b2981
@anoronh4
add poison pill to reference channels
7325589
@anoronh4
update md5sum in test_profile test
c204119
@anoronh4
update ensembl version to 112
7c5dc28
@anoronh4
update CHANGELOG.md
d8e423f
@anoronh4
change ensembl version to 111
4966057
@anoronh4
update AGFusion to [email protected]
3bbaecf
@anoronh4
fix conflicts
3ea6c20
@anoronh4
Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into…
29f10aa 
… enhancement/hg38_update
@anoronh4
add cpus in AGAT_SPADDINTRONS resources
cd06afc
@anoronh4
fix indentation
3bfeb91
@pintoa1-mskcc
Set gene_id as gene_name for lncRNAs, remove NF transcripts from gene…
9147321 
… bed
@anoronh4
Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into…
6e09888 
… enhancement/hg38_update
@pintoa1-mskcc
fix linting error, ensure no scientific notation in gene bed
ad50743
@pintoa1-mskcc
Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into…
db34bad 
… enhancement/hg38_update
@anoronh4 anoronh4 marked this pull request as ready for review October 9, 2024 18:38
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I’ll have to make a separate function for gene bed generation because v111 has “five_prime_utr” and “three_prime_utr”, whereas v75 just has UTR. Currently the gene bed for hg38 is lacking UTRs due to this

huyu335
huyu335 approved these changes Nov 21, 2024
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Tested on clinical prod cluster, looks good!

carynhale
carynhale approved these changes Nov 22, 2024
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I have tested this quite a bit on crater2 and am using it for validation samples currently, no major issues.

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@huyu335 huyu335 huyu335 approved these changes

@carynhale carynhale carynhale approved these changes

@pintoa1-mskcc pintoa1-mskcc Awaiting requested review from pintoa1-mskcc

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update for GRCh38
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@anoronh4 @pintoa1-mskcc @carynhale @huyu335