Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update/metafusion #126

Merged
merged 57 commits into from
Jan 30, 2025
Merged

Update/metafusion #126

merged 57 commits into from
Jan 30, 2025

Conversation

pintoa1-mskcc
Copy link
Collaborator

@pintoa1-mskcc pintoa1-mskcc commented Sep 18, 2024 •
edited
Loading

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. Additionally this branch includes a bugfix/cff_split_span where split reads for arrriba is calculated using split1 and split2 from arriba and FC split reads is -1 (as FC does not calculate split)
  • 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
@pintoa1-mskcc
Copy link
Collaborator Author

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
@pintoa1-mskcc
Copy link
Collaborator Author

Reminder to check problematic chromosomes for metafusion now that we are using decoy sequences in grch38

@pintoa1-mskcc pintoa1-mskcc changed the base branch from develop to enhancement/hg38_update November 12, 2024 20:00
@anoronh4 anoronh4 requested review from carynhale and huyu335 January 10, 2025 18:07
carynhale
carynhale approved these changes Jan 10, 2025
View reviewed changes
Copy link
Collaborator

@carynhale carynhale left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I have tested this branch on crater2, everything looks good to me as far as outputs go.

@pintoa1-mskcc pintoa1-mskcc dismissed anoronh4’s stale review January 17, 2025 17:10

Updated from comments

@pintoa1-mskcc pintoa1-mskcc changed the base branch from enhancement/hg38_update to develop January 17, 2025 17:12
anoronh4
anoronh4 requested changes Jan 21, 2025
View reviewed changes
Copy link
Collaborator

@anoronh4 anoronh4 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

hopefully pretty small changes. overall we are pretty close i think.

conf/igenomes.config Show resolved Hide resolved
bin/add_flags_and_cluster_information.R Outdated Show resolved Hide resolved
subworkflows/local/prepare_references.nf Outdated Show resolved Hide resolved
modules/local/metafusion/run/main.nf Outdated Show resolved Hide resolved
modules/local/metafusion/container/Dockerfile Outdated Show resolved Hide resolved
subworkflows/local/fusion.nf Outdated Show resolved Hide resolved
huyu335
huyu335 approved these changes Jan 24, 2025
View reviewed changes
Copy link
Collaborator

@huyu335 huyu335 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Tested on clinical production cluster. Looks good!

@anoronh4 anoronh4 merged commit c3b1e72 into develop Jan 30, 2025
6 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@anoronh4 anoronh4 anoronh4 approved these changes

@carynhale carynhale carynhale approved these changes

@huyu335 huyu335 huyu335 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@pintoa1-mskcc @anoronh4 @carynhale @huyu335