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mskcc
NeoQual-nf
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Feature/release candidate 2.0.0
- #97
#97
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nikhil
wants to merge 49 commits into
dev
mskcc/NeoQual-nf:dev
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Feature/release candidate 2.0.0
#97
nikhil
wants to merge 49 commits into
dev
mskcc/NeoQual-nf:dev
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feature/release_candidate_2.0.0
mskcc/NeoQual-nf:feature/release_candidate_2.0.0
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Commits on Apr 23, 2026
Config changes for release 2.0.0
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Commits on May 8, 2026
Exclude conda in tests
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Commits on May 21, 2026
Merge branch 'dev' of github.com:mskcc/neoantigen-pipeline into feature/release_2.0.0
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Commits on Aug 11, 2026
chore: sync SV-channel-padding subworkflows and pin to merged develop
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fix: pin iedb.fasta to an immutable commit instead of a branch ref
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fix: give PHYLOWGS_MULTIEVOLVE a walltime that can actually cover it
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Commits on Aug 20, 2026
chore(modules): sync neoantigen-utils-base 1.6.1 + PhyloWGS resume support
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Commits on Aug 24, 2026
fix(neoantigeninput): pin to :1.6.1-amd64 to work around stale GHCR manifest
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fix(neoantigeninput): redirect pyensembl cache off $HOME on iris
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feat(neoantigeninput): add --pyensembl_cache_dir to share the pyensembl index
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Commits on Aug 25, 2026
fix(neoantigenediting): pin to :1.1-amd64 to work around stale GHCR manifest
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fix(aligntoiedb): use --sample_file, not --input, matching the baked-in script's CLI
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fix(computefitness): match compute_fitness.py's rewritten CLI, add compute_fitness_kd_cutoff
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fix(createinput): skip leading '#' metadata lines when parsing MAF
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Commits on Aug 26, 2026
feat(multievolve): add per-sample walltime config, capped to cmobic_cpu's 7d MaxTime
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Added args to phylowgs to reduce time for checkpointing. THis reduces IO usage on the cluster
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Commits on Sep 2, 2026
Revert "fix(neoantigenediting): pin to :1.1-amd64 to work around stale GHCR manifest"
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Revert "fix(neoantigeninput): pin to :1.6.1-amd64 to work around stale GHCR manifest"
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Commits on Sep 10, 2026
Module update
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Update iedbfasta URL in juno.config
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Update iedbfasta URL in test.config
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Update iedbfasta URL in production config
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Added subworkflows
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Template update for nf-core/tools version 4.1.0
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Template update for nf-core/tools version 4.1.0
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Merge branch 'TEMPLATE' into feature/release_candidate_2.0.0
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Linting fix
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Updated configs
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Update test and snap
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Commits on Sep 11, 2026
Change name from neoantigenpipeline to NeoQual-nf
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Merge branch 'TEMPLATE' of github.com:mskcc/neoantigen-pipeline into TEMPLATE
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Rename neoantigenpipeline to neoQual-nf
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Added kd_cutoff fitness
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Change NFT_WORKDIR to use runner.temp directory
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Fix linting for tests
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Ignore a few tests
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Fixed linting errors
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Merge branch 'TEMPLATE' of github.com:mskcc/neoantigen-pipeline into feature/release_candidate_2.0.0
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Merge branch 'feature/release_candidate_2.0.0' of github.com:mskcc/neoantigen-pipeline into feature/release_candidate_2.0.0
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Update nf-core yml
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Some more linting fixes
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Fix NFT_WORKDIR syntax in nf-test.yml
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Switch NFT_WORKDIR path
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Fix snap file
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Merge branch 'feature/release_candidate_2.0.0' of github.com:mskcc/neoantigen-pipeline into feature/release_candidate_2.0.0
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Update snap
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Remove non-deterministic files from checksum verification
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Fix snap file
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Add non-deterministic files to .nftignore
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