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Update/metafusion #126

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Update/metafusion #126

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pintoa1-mskcc
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@pintoa1-mskcc pintoa1-mskcc commented Sep 18, 2024 •
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PR checklist

  • Enable use of modified metafusion to prioritise refseq clinical genes (docker image 0.0.8). Also modifies gene bed to be 0 based and removed not finished transcripts from gene bed file.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Noronha and others added 30 commits January 19, 2024 11:39
update metafusion to 1.0.2
b8fd25b
@pintoa1-mskcc
Clinical Transcripts Added to Params/metafusion, added clinical names…
cc97342 
… to add flag function
@pintoa1-mskcc
add clinical whitelist to assests
181ec3a
@pintoa1-mskcc
Update igenomes.config assets
0b3e019
@pintoa1-mskcc
Update igenomes.config
ddc4f49
@pintoa1-mskcc
Update igenomes.config
0c40229
@pintoa1-mskcc
terra configuration for references
c52013b
@pintoa1-mskcc
Merge branch 'update/metafusion' into update/terra
1a2e35c
@pintoa1-mskcc
Merge pull request #108 from mskcc/update/terra
2f4dfb9 
Add terra config to update metafusion branch
@pintoa1-mskcc
Merge branch 'enhancement/produce_metafusion_ref' into update/metafusion
9b8bf0a
@pintoa1-mskcc
mrge prepare metafusion references and update metafusion
e987538
@pintoa1-mskcc
modify metafusion transcripts to include transcript version
efe528e
@pintoa1-mskcc
Merge remote-tracking branch 'origin/develop' into update/metafusion
eef5d0b
@pintoa1-mskcc
move adding transcript versions to during cff annotate so agfusion ca…
d227e1e 
…n run
@pintoa1-mskcc
editor config
791241f
@pintoa1-mskcc
move merge of transcripts to after merge with agfusion
a4a71a4
@pintoa1-mskcc
try to resolve pr conflicts
5ac50c3
@pintoa1-mskcc
prettier readme
6a9c245
@pintoa1-mskcc
modify modules/local/metafusiongenebed bin
64de02a
@pintoa1-mskcc
add gff2bed step for metafusion genebed generation
1bcb409
@pintoa1-mskcc
match develop
b623d21
@pintoa1-mskcc
revert use of BED, change gtf to 0 based start
1264001
@pintoa1-mskcc
full revert of use of genebed in metafusion ref generation
f4b896a
@pintoa1-mskcc
gtf should be gff to match previous
9cb8943
@pintoa1-mskcc
Rename clinical file, update metafusion docker
35f1f78
@pintoa1-mskcc
Merge branch 'develop' into update/metafusion
a210c65 
Match develop branch
@pintoa1-mskcc
New version of metafusion_forte.sh
b215852
@pintoa1-mskcc
remove terra designation, change metafusion docker version
d906a0c
@pintoa1-mskcc
Fix NA values in final CFF
6823a24
@pintoa1-mskcc
Clean up flagging and versions of transcripts
dba6361
anoronh4
anoronh4 approved these changes Sep 19, 2024
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anoronh4
anoronh4 requested changes Sep 19, 2024
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did not mean to approve, needs changes.

@pintoa1-mskcc
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I'm going to wait to push this PR until I can merge the hg38 branch in and provide some edits for that

@pintoa1-mskcc pintoa1-mskcc reopened this Oct 2, 2024
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Reminder to check problematic chromosomes for metafusion now that we are using decoy sequences in grch38

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@anoronh4 anoronh4 Awaiting requested review from anoronh4

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