nf-core/epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for the reference genome and VEP offline cache used for variant annotation.
Reference genome FASTA matching the build (Ensembl primary assembly, contigs 1..MT), plain or bgzipped, with a .fai (and .gzi) index alongside. Required for variant (VCF) input unless –vep_download_cache is set.
stringPath to the VEP offline Ensembl cache. Either the cache directory or a .tar.gz of it. Required for variant input unless –vep_download_cache is set.
stringVEP cache version, matching the downloaded cache (e.g. 110). Required for variant input.
integerVEP species, matching the cache (e.g. homo_sapiens, mus_musculus). Required for variant input.
stringVEP assembly, matching the cache (e.g. GRCh38, GRCm39). Required for variant input.
stringDownload the VEP cache and reference FASTA in-pipeline instead of providing –vep_cache/–ref_fasta.
booleanOptions for the peptide prediction step.
Specifies the column name in the input file that contains the peptide sequences.
stringsequenceSpecifies the minimum peptide length.
integer8Specifies the maximum peptide length.
integer12Specifies the minimum peptide length for MHC class II peptides.
integer8Specifies the maximum peptide length for MHC class II peptides.
integer25Specifies the prediction tool(s) to use.
stringmhcnuggetsSpecifies whether wild-type sequences should be predicted.
booleanOptional reference proteome FASTA for self-filtering variant peptides.
stringNumber of amino acids flanking the mutation on each side in the published variant protein FASTA (variant_fasta/); frameshifts run to the new stop.
integer25Specifies that the output file will be in wide format.
booleanFilter out non-binders from the final results.
booleanUse BA_Rank instead of EL_Rank for netMHCpan and netMHCIIpan predictions.
booleanOptions for optimising the pipeline run execution.
Specifies the maximum number of peptide chunks.
integer100Specifies the minimum number of peptides that should be written into one chunk.
integer5000External MHC binding prediction software that is not shipped with the pipeline.
Specifies the path to the JSON file with meta information on external prediction tools.
stringSpecifies the operating system in use (Linux or Darwin). This is only necessary if conda is used.
stringTo use the ‘netmhcpan’ tool, specify the path to the original software tarball for NetMHCpan 4.0 here.
string^\S+\.tar\.gz$To use the ‘netmhciipan’ tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here.
string^\S+\.tar\.gz$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
boolean