Nextflow module for Neoantigen editing - compute_fitness.py - Githubissues

mskcc / neoantigen-pipeline

Pipeline for computing neoantigen qualities from DNA and RNA-Seq data

MIT License

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Nextflow module for Neoantigen editing - compute_fitness.py #17

Closed nikhil closed 6 months ago

nikhil commented 8 months ago

Dockerhub Container: mskcc/neoantigenediting:1.0 command: python /usr/bin/compute_fitness.py The workdir needs to have the input in a data folder of the structure

data/id_1/id_2/Patient_data

where id_1 can be the patient and id_2 can be the sample id

and

data/iedb.fasta

and

data/IEDB_alignments generated from the previous step

see https://github.com/LukszaLab/NeoantigenEditing/tree/main/data

The output is data/id_1/id_2/Patient_data_annotated.json