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docs: update fusionreport score calculation documentation #1

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docs: update fusionreport score calculation documentation #1

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KuthuruTejaswini
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Resolves nf-core#555

Updates documentation to reflect new fusionreport score calculation:

  • Added detailed explanation of new scoring system
  • Documented 80/20 weight distribution between tool detection and database hits
  • Added formula for score calculation

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 necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: CONTRIBUTING.md

alanmmobbs93 and others added 30 commits December 5, 2024 14:25
@alanmmobbs93
update test for skipping fastp
e033e94
@alanmmobbs93
update changelog
8f3c70e
@atrigila
fix: change hardcoded container for seqera container, mv conda to env…
cc916e6 
…ironment.yml
@atrigila
docs: update changelog
2010578
@atrigila
fix: specify version 1.33 in bioconda and seqera container
ca0870b
@alanmmobbs93
add new test
90aced2
@alanmmobbs93
Merge pull request nf-core#572 from alanmmobbs93/trim_workflow_test
e2a255b 
Add nf-test to TRIM_WORKFLOW
@nschcolnicov
Merge pull request nf-core#550 from nf-core/general_fixes
8e1aa7e 
Updated tests and fusion containers and conda versions, general confi…
@atrigila
refactor: emit a directory and add meta
6189acf
@atrigila
test: add fusionreport nf-test
2620dcf
@alanmmobbs93
update module
9673b85
@alanmmobbs93
update subworkflow
275889e
@apeltzer
Merge pull request nf-core#574 from alanmmobbs93/update_arriba-arriba…
a7e1b53 
…_module

Update arriba_arriba module
@rannick
update fusioncatcher container
d290fcd
@rannick
Merge branch 'refactor-references' of https://github.com/nf-core/rnaf…
19757b6 
…usion into refactor-references
@atrigila
test: add test to FUSIONREPORT_DETECT
75b65f7
@atrigila
docs: update changelog
2c860bb
@alanmmobbs93
change module structure and first test attempt
e80fd83
@alanmmobbs93
update test and generate first snap
a6c082e
@rannick
fix merge conflicts
1a1314e
@rannick
fix linting issues
be6e102
@rannick
prettier
41523f9
@alanmmobbs93
update tests after fixing fasta in github
55b0562
@alanmmobbs93
update changelog
55db5b5
@atrigila
Merge pull request nf-core#573 from atrigila/fusioncatcher_download
739c482 
Change `FUSIONCATCHER_DOWNLOAD` docker image to Seqera container
@atrigila
docs: udpdate changelog
ce331dc
@atrigila
Merge branch 'dev' into fusionreport_detect
54b1932
@atrigila
test: update nf-test
d7a06ea
@alanmmobbs93
update test excluding samtools
df269a9
@alanmmobbs93
Merge branch 'dev' into add_test_arriba_workflow
715be91 
merge dev branch
atrigila and others added 24 commits January 8, 2025 09:37
@atrigila
Merge branch 'dev' into create_nftest_build_references
c02735f
@atrigila
test: adapt the test to new template
f976de1
@atrigila
test: try fix on template merge issue
2a2d9ca
@atrigila
Merge pull request nf-core#605 from atrigila/create_nftest_build_refe…
9fe3e10 
…rences

Add pipeline-level nf-test (`BUILD_REFERENCES`)
@atrigila
Merge pull request nf-core#601 from atrigila/fusioninspector_nftest
9fd122e 
Add nf-test for local module `FUSIONINSPECTOR`
@atrigila
Merge branch 'dev' into fusionreport_workflow_nftest
d17422d
@atrigila
test: update tests and snapshot
b7c928b
@atrigila
docs: update changelog
675c0a3
@nf-core-bot
Template update for nf-core/tools version 3.1.2
7bfea34
@rannick
Merge branch 'dev' into nf-core-template-merge-3.1.2
7e9a778
@rannick
remove md5sums for databases
9fcd72f
@rannick
move outdir up
cf53a21
@rannick
update changelog
49b2e1d
@rannick
excude databases subject to quick changes
77952f9
@rannick
Merge pull request nf-core#609 from nf-core/nf-core-template-merge-3.1.2
e177b3a 
Important! Template update for nf-core/tools v3.1.2
@rannick
Merge branch 'dev' into error_output_missing
e69f0a5
@rannick
Merge branch 'dev' into fusionreport_workflow_nftest
9961a12
@rannick
Merge pull request nf-core#611 from nf-core/error_output_missing
42ed785 
Fix error when output is missing
@rannick
Merge branch 'dev' into fusionreport_workflow_nftest
e138e7f
@atrigila
fix: add unstable files to nftignore
2d5d9bb
@atrigila
Merge pull request nf-core#607 from atrigila/fusionreport_workflow_nf…
1cb14de 
…test

Add nf-test for `fusionreport_workflow` subworkflow
@nf-core-bot
Template update for nf-core/tools version 3.2.0
6d6fbe9
@rannick
Merge branch 'dev' into nf-core-template-merge-3.2.0
4360f1b
@rannick
Merge pull request nf-core#615 from nf-core/nf-core-template-merge-3.2.0
b9d8337 
Important! Template update for nf-core/tools v3.2.0
@KuthuruTejaswini
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This PR addresses the documentation updates requested in that issue nf-core#555

@atrigila
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Hi @KuthuruTejaswini, could you make this PR against the dev branch of https://github.com/nf-core/rnafusion? Currently it is against rannick's fork. Thank you.

@KuthuruTejaswini KuthuruTejaswini force-pushed the docs/update-fusionreport-score branch from defd621 to 8906966 Compare February 21, 2025 01:07
@dacotah03
docs: update fusionreport score calculation documentation
659fa0b 
- Add detailed explanation of new scoring system
- Document 80/20 weight distribution between tool detection and database hits
- Add formula for score calculation
@KuthuruTejaswini KuthuruTejaswini force-pushed the docs/update-fusionreport-score branch from 8906966 to 659fa0b Compare February 21, 2025 01:20
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Documentation should reflect fusionreport score metric change
9 participants
@KuthuruTejaswini @atrigila @alanmmobbs93 @nschcolnicov @apeltzer @rannick @nf-core-bot @nvnieuwk @dacotah03