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Release/0.1.1 #130

Merged
merged 552 commits into from
Aug 28, 2024
Merged

Release/0.1.1 #130

merged 552 commits into from
Aug 28, 2024

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buehlere
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PR for release/0.1.1

  • editor config fix

  • add README

  • modules added:

    • phylowgs/createinput
    • phylowgs/parsecnvs
    • phylowgs/multievolve
    • phylowgs/writeresults
    • netmhcpan
    • neoantigeninput
    • neoantigenediting/aligntoIEDB
    • neoantigenediting/computeFitness
    • netmhcstabpan
    • ppflagfixer
    • neoantigenutils/generatemutfasta
    • neoantigenutils/formatnetmhcpan
    • neoantigenutils/generatehlastring
    • neoantigenutils/neoantigeninput
    • salmon/index
    • genomenexus/vcf2maf
    • genomenexus/annotationpipeline
    • ppflagfixer
    • pvmaf/tagtraceback
    • pvmaf/concat
    • genotypevariants/all
    • salmon/index
    • salmon/quant
    • rediscoverte

  • subworkflows added:

    • subworkflows/phylowgs
    • subworkflows/genome_nexus
    • subworkflows/neoantigen_editing
    • subworkflows/netmhcstabandpan
    • subworkflows/traceback

buehlere and others added 30 commits April 18, 2024 15:42
@buehlere
Merge branch 'develop' into fix/pytest_yml
77025d0
@buehlere
Merge pull request #90 from mskcc-omics-workflows/fix/pytest_yml
f113d89 
Fix/pytest yml
fix editorconfig linting errors
e8efb40
fix snapshot
08bb8db
fix snapshot
e706813
@anoronh4
Merge branch 'develop' into update/editorconfig_config
4bb68cf
@anoronh4
Merge pull request #88 from mskcc-omics-workflows/update/editorconfig…
e82f7ff 
…_config

add .editorconfig file
@nikhil
Merge branch 'develop' of github.com:mskcc-omics-workflows/modules in…
f5c1db7 
…to neoantigen
@nikhil
Merge branch 'neoantigen' into feature/netMHCstabpan
8a0dc67
@nikhil
Merge pull request #85 from mskcc-omics-workflows/feature/netMHCstabpan
0476a13 
Feature/netmhcstabpan
@nikhil
Merge branch 'neoantigen' of github.com:mskcc-omics-workflows/modules…
eba93db 
… into feature/merge_with_dev
@nikhil
Remove trailing whitespace
9370ea3
@nikhil
Merge pull request #91 from mskcc-omics-workflows/feature/merge_with_dev
6656bdb 
Merge with dev
@huyu335
Merge branch 'develop' into feature/ppflagfixer
32d7a9e
@huyu335
Remove empty line
acc2542
@huyu335
Update test data mskcc
3a7aedf
@huyu335
update test datasets
cd0564b
@nikhil
Moved neoantigeninput to neoantigenutils
dccb7d5
@nikhil
Refactor netmhcpan
df124ae
@nikhil
Refactore netmhcstabpan
4bfadff
@nikhil
Updated test data
f956361
@nikhil
Add formatnetmhcpan neoantigenutils module
57efd11
@nikhil
Add generatehlastring neoantigenutils module
bbf7fb6
@nikhil
Add generatemutfasta neoantigenutils module
a7d2736
@nikhil
Add netmhcstabandpan subworkflow
10da51f
@nikhil
Fix ECLint
4c9ae8f
@nikhil
Add conda skips
7b49ce2
@nikhil
Fix meta yml documentation links
c3ede79
@nikhil
Ignore conda test for subworkflow
6c9ca3c
@nikhil
Fix name for linting
332dacb
johnoooh and others added 23 commits July 24, 2024 16:21
@johnoooh
more linting
5c72f8c
@johnoooh
Update environment.yml
373f2ca
@johnoooh
Updating version file
62288ed
@johnoooh
new version out
3d98438
@johnoooh
test fix ?
5ca84b1
@buehlere
Merge pull request #47 from mskcc-omics-workflows/Subworkflow-traceback
8eaf1be 
Subworkflow:traceback
@rnaidu
changed versioning of annotation pipeline module in genome nexus subw…
2c02998 
…orkflow to latest release
@nikhil
Merge branch 'develop' into feature/neoTSV
c9d0b61
@rnaidu
working tests for annotationpipeline after updating versioning
903010e
@buehlere
Merge branch 'develop' into hotfix/update-test-datasets
0b36e74
@rnaidu
Merge pull request #118 from mskcc-omics-workflows/genomenexus_versio…
4cc20e2 
…ning

changed versioning of annotation pipeline module in genome nexus subw…
@nikhil
Update java vm args
c3a6acc
@rnaidu
Merge pull request #121 from mskcc-omics-workflows/feature/update_jav…
7891d1a 
…a_vm_args

Update java vm args
@huyu335
Merge branch 'develop' into feature/ppflagfixer
db0b943
@huyu335
Merge pull request #43 from mskcc-omics-workflows/feature/ppflagfixer
eaabe46 
Module:ppflagfixer
@huyu335
Merge branch 'develop' into hotfix/update-test-datasets
c044b75
@nikhil
Fix stub test for formatnetmhcpan
c5d1252
@nikhil
Merge branch 'develop' into feature/fix_formatnetmhcpan_stub_test
d602115
@johnoooh
Merge pull request #123 from mskcc-omics-workflows/feature/fix_format…
4b3b452 
…netmhcpan_stub_test

Fix stub test for formatnetmhcpan
@johnoooh
Merge branch 'develop' into feature/neoTSV
2d435c4
@johnoooh
Merge pull request #117 from mskcc-omics-workflows/feature/neoTSV
5863d3d 
Feature/neo tsv
@huyu335
Merge branch 'develop' into hotfix/update-test-datasets
68ae56e
@huyu335
Merge pull request #92 from mskcc-omics-workflows/hotfix/update-test-…
6f7f20d 
…datasets

Hotfix/update test dataset links
@buehlere buehlere requested a review from a team as a code owner August 26, 2024 14:29
@buehlere buehlere merged commit 6513ff7 into main Aug 28, 2024
136 of 141 checks passed
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@rhshah rhshah rhshah approved these changes

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7 participants
@buehlere @rhshah @anoronh4 @nikhil @huyu335 @johnoooh @rnaidu