How To Run

1. Create sample-specifc config file using the template

2. Create a sample-specific input CSV file using this template when using GVF or variant FASTA as entrypoint or this template when using raw variant files.

3. To run on UCSL-CDS' Azure clusters, see the submission script, here, to submit it. For general usage, launch with the command below:

nextflow run path/to/pipeline-call-NoncanonicalPeptide/main.nf -c sample.config

:warning: This pipeline should only run one sample at a time. The input CSV file should only contain one sample and all mutation files associated with the one sample.

:information_source: The pipeline requires the genomic reference index generated by the moPepGen generateIndex command. See here for the usage of this command.

:information_source: Novel-ORF peptides and alt-translation peptides can be provided into this pipeline for splitting, encoding, and creating decoy databases. They can be generated using the callNovelORF and callAltTranslation command from moPepGen.

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