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.
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Options for the genome and proteome reference.
Specifies the Ensembl genome reference version that will be used.
string
grch37
Specifies the reference proteome fasta file that is used for self-filtering peptides derived from provided genomic variants.
string
Options for the peptide prediction step.
Specifies the column name in the input file that contains the peptide sequences.
string
sequence
Specifies the minimum peptide length.
integer
8
Specifies the maximum peptide length.
integer
12
Specifies the minimum peptide length for MHC class II peptides.
integer
8
Specifies the maximum peptide length for MHC class II peptides.
integer
25
Specifies the prediction tool(s) to use.
string
mhcnuggets
Specifies whether wild-type sequences should be predicted.
boolean
Specifies that sequences of proteins, affected by provided variants, will be written to a FASTA file.
boolean
Specifies that the output file will be in wide format.
boolean
Options for optimising the pipeline run execution.
Split VCF file into multiple files by number of variants.
boolean
Number of variants that should be written into one file. Default: number of variants divided by ten
integer
Number of nucleotides between previous and current variant across split.
integer
110000
Specifies the maximum number of peptide chunks.
integer
100
Specifies the minimum number of peptides that should be written into one chunk.
integer
5000
External 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.
string
Specifies the operating system in use (Linux or Darwin). This is only necessary if conda is used.
string
To 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.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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.
string