Neoantigen Merge to get some neoantigen branch updates#244
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Bash <<- operator only strips leading tabs, not spaces. NF 25.04.0 does not apply stripIndent() to command blocks before writing .command.sh, so space-indented heredoc content is not recognized. Convert heredoc content lines and END_VERSIONS terminator to use tab indentation, which works correctly with both NF 25.04.0 and later versions that apply stripIndent(). Also replace deprecated new Tuple() constructor calls with Groovy list literals in subworkflows for NF 26.x forward compatibility. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Restores 19 non-pipeline modules to their develop state. Only the 16 modules and 3 subworkflows used by the neoantigen pipeline retain the NF 25.04.0 heredoc tab-indentation fix. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…whitespace Update neoangtiegen modules to work with nf-core pipeline testing
This reverts commit e01dcb9.
…tigen_input_resource Increased resouce for neoantigen input
…meta Update file patterns in meta.yml for SV sequences
- C1: Guard empty score_list and zero Kd/KdWT in compute_fitness.py - C2: Add amino acid X support, missing-key guards, and variable-length epitope distance in EpitopeDistance.py - C3: BioPython PairwiseAligner fallback, empty alignment guard, and uppercase normalization in align_neoantigens_to_IEDB.py - C4: Initialize PTC_exon before loop and guard None best_pepmatch2 in generate_input.py - C5: Fix "nonsense_nutation" typo in generate_input.py and generateMutFasta.py - I4: Replace destructive `cat >> inputFasta` with safe `cat > combined_input.fa` in netmhcpan4 and netmhcstabpan modules - I5: Close leaked out_WT_fa file handle in generateMutFasta.py Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Keep only the amino acid X addition and docstring update. Revert set_model() error handling and variable-length epitope_dist() changes per review feedback. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Drop amino acid X and docstring change — the model JSON lacks X->* entries, causing KeyError at runtime. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…alyzer_retriever Add verbose compression type checks for mutalyzer retriever
Replace `I+`/`I-` in variant_type_map with `Fi`/`Fd` so that downstream MHC tools (which sanitize special characters) cannot collapse two distinct frameshift classes onto the same `I_` token, which previously caused a KeyError in generate_input.py when looking up the original key in mutation_dict. Changes: - generateMutFasta.py / generate_input.py: variant_type_map values `I+` -> `Fi` (frame_shift_ins), `I-` -> `Fd` (frame_shift_del). - generate_input.py: `IDsplit[1][0] != \"I\"` widened to also exclude the new `F` prefix so frameshifts continue to take the indel branch rather than the missense-polymorphism branch. Frameshift detection switched from `+`/`-` substring check to `Fi`/`Fd` prefix check. - Refresh nf-test snapshots (neoantigeninput json,tsv md5; generatemutfasta versions.yml md5). Companion: test fixture rename in mskcc-omics-workflows/test-datasets (neoantigen branch).
Fix PR #87 review issues: Python bug fixes and .nf module safety
nikhil
approved these changes
May 7, 2026
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Closes #XXX
feature/<module_name>for modules, orfeature/<subworkflow_name>for subworkflows. For modules, if there is a subcommand use:feature/<module_name>/<module_subcommand>.versions.ymlfile.label.nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile dockernf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularitynf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile condanf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile dockernf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularitynf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda