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Release candidate for 1.0.0 #46

Merged
merged 134 commits into from
Jul 31, 2024
Merged

Release candidate for 1.0.0 #46

merged 134 commits into from
Jul 31, 2024

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nikhil
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@nikhil nikhil commented Jul 8, 2024

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

nikhil and others added 30 commits March 20, 2024 17:07
@nikhil
Install modules from mskcc-omics repo
ba48b39
@nikhil
Add references to main pipeline
fd5ae9f
@johnoooh
Changed README description, input samplesheet
fd18a97 
preparing for subworkflow inclusion
@johnoooh
Added new subworkflows, updated modules, added netmhcstabpan
c301d21
@johnoooh
changed from capital to lowercase
6b2e638
@johnoooh
iedb moved test
2634a7c
@johnoooh
computeFitness -> computefitness
bdd79a0
@nikhil
Merge pull request #32 from mskcc/subworkflows
d885385 
Subworkflows merge test
@johnoooh
Update schema_input.json
ae24c58
@johnoooh
Update README.md
ecc94e9
@johnoooh
Update samplesheet.csv
3e7fc50
@johnoooh
Update schema_input.json
0c92a5a 
tempo_maf -> maf for clarity
@nikhil
Merge pull request #33 from mskcc/inputschema
d30453a 
Input schema changes from nf-core default to new schema
@johnoooh
Adding netmhcpan
8c0067d 
netmhcstabpan still in development
@nikhil
Merge pull request #34 from mskcc/feature/netmhcpan
4201620 
Adding netmhcpan
@johnoooh
test profile added, running currently
8f9a743 
nf-test added but not yet working.  Neoantigen pipeline almost assembled.  Just need to add neoantigenediting.

Lots more to do
@johnoooh
Multievolve chain reduction
90fb313
@nikhil
Ignore .nf-test.log
ab6e02c
@johnoooh
Pipeline workign with some changes to modules
a37480b 
Changes incoming
@johnoooh
Module fixes
9ae2173
@johnoooh
neoantigen input update
a6c2a37
@johnoooh
Neoantigenediting
dbc08f4
@johnoooh
netmhcpan test update
8140428
@nikhil
Set process to medium
e8eeeab
@nikhil
Update neoantigeninput
402083d
@nikhil
Some cleanup
0d8620b
@nikhil
Add github action
6bd4ce0
@nikhil
Update test config to have relative path
e8eb64f
@nikhil
Add github action
44a796b
@johnoooh
Update README.md
4e0b6b0 
Added workflow steps to introduction.
johnoooh and others added 26 commits July 8, 2024 16:15
@johnoooh
Adding picture, removing old fastqc pics
7b199ae
update parse cnvs
463fd5e
@nikhil
Made code prettier 🌸
4f9297e
@nikhil
Removed unused modules
6658df8
@nikhil
Made code prettier (again) 🌷
53700ac
@nikhil
Update modules json
4764cf1
@nikhil
Re-enable download_pipeline.yml
b20ccbc
@nikhil
Set relative path to samplesheet
115c18d
@nikhil
Use double quotes instead
8e450cf
@nikhil
Update input for test config
21be037
@nikhil
Update test.config
d6fec2c
@johnoooh
Merge pull request #48 from mskcc/feature/update_input_samplesheet_path
0aa3a64 
Update input for test config
@nikhil
Merge pull request #49 from mskcc/dev
d82ec09 
Update pipeline download test
@nikhil
Update to use modules from develop
5df2593
@nikhil
Cleanup EpitopeDistance.py
23e53ba
@nikhil
Merge pull request #50 from mskcc/feature/update_modules_to_base_develop
7f820a8 
Feature/update modules to base develop
@nikhil
Merge pull request #51 from mskcc/dev
ab09ea5 
Dev
@nikhil
Add master PR for ci tessts
937e08d
@nikhil
Add master PR for ci tests
c915eb1
@nikhil
Merge branch 'release/candidate-1.0.0' of github.com:mskcc/NeoAntigen…
ca817ab 
…-Pipeline into release/candidate-1.0.0
@johnoooh
Update usage.md
2d482fe 
edited usage doc
@johnoooh
Update usage.md
43ed419
@johnoooh
Update .editorconfig
60d772b
@johnoooh
Update usage.md
c50005d
@johnoooh
Update .editorconfig
18c10f7
@nikhil
Made docs code prettier
53eedf9
johnoooh
johnoooh approved these changes Jul 31, 2024
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Go team!

pintoa1-mskcc
pintoa1-mskcc approved these changes Jul 31, 2024
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Great job guys

@nikhil nikhil merged commit 18769d6 into master Jul 31, 2024
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@nikhil nikhil deleted the release/candidate-1.0.0 branch July 31, 2024 14:49
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@johnoooh johnoooh johnoooh approved these changes

@pintoa1-mskcc pintoa1-mskcc pintoa1-mskcc approved these changes

@arichards2564 arichards2564 Awaiting requested review from arichards2564

@BradicM BradicM Awaiting requested review from BradicM

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3 participants
@nikhil @johnoooh @pintoa1-mskcc