github.com/nf-core/epitopeprediction

A fully reproducible and state of the art epitope prediction pipeline. Usage: The typical command for running the pipeline is as follows: nextflow run nf-core/epitopeprediction -profile --input "*.vcf.gz" Mandatory arguments: --input Path to input data (must be surrounded with quotes) --alleles Path to the file containing the MHC alleles -profile Configuration profile to use. Can use multiple (comma separated) Available: conda, docker, singularity, awsbatch, test and more Alternative inputs: --peptides Path to TSV file containing peptide sequences (minimum required: id and sequence column) Pipeline options: --filter_self Specifies that peptides should be filtered against the specified human proteome references Default: false --wild_type Specifies that wild-type sequences of mutated peptides should be predicted as well Default: false --mhc_class Specifies whether the predictions should be done for MHC class I or class II. Default: 1 --max_peptide_length Specifies the maximum peptide length Default: MHC class I: 11 aa, MHC class II: 16 aa --min_peptide_length Specifies the minimum peptide length Default: MCH class I: 8 aa, MHC class II: 15 aa --tools Specifies a list of tool(s) to use. Available are: 'syfpeithi', 'mhcflurry', 'mhcnuggets-class-1', 'mhcnuggets-class-2'. Can be combined in a list separated by comma. References If not specified in the configuration file or you wish to overwrite any of the references --genome Specifies the ensembl reference genome version (GRCh37, GRCh38) Default: GRCh37 --proteome Specifies the reference proteome(s) used for self-filtering Other options: --outdir The output directory where the results will be saved --email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits -name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. --max_multiqc_email_size Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB) AWSBatch options: --awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch --awsregion The AWS Region for your AWS Batch job to run on