├── Dockerfile ├── README.md ├── assets ├── Mods.txt └── workflow.png ├── bin ├── calculate_phastcons.py ├── calculate_phylocsf.py ├── extract_1mismatch_novpsm.py ├── group_novpepToLoci.py ├── label_nsSNP_pep.py ├── label_sub_pos.py ├── map_cosmic_snp_tohg19.py ├── map_novelpeptide2genome.py ├── parse_BLASTP_out.py ├── parse_BLAT_out.py ├── parse_annovar_out.py ├── parse_spectrumAI_out.py ├── peptide_pi_annotator.py ├── pi_database_splitter.py ├── reverse_decoy.py └── scan_bams.py ├── conf ├── base.config ├── sixft.config └── uppmax.config ├── envs └── environment.yml ├── main.nf └── nextflow.config /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lehtiolab/proteogenomics-analysis-workflow/HEAD/Dockerfile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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