nf-core/epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
2.1.0). The latest
stable release is
3.0.0
.
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^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for the genome and proteome reference.
Specifies the human reference genome version.
stringSpecifies the reference proteome.
stringReference genome related files and options required for the workflow.
Do not load the iGenomes reference config.
booleanOptions for the peptide prediction step.
Filter against human proteome.
booleanSpecifies the maximum peptide length.
integer11Specifies the minimum peptide length.
integer8Specifies the maximum peptide length for MHC class II peptides.
integer16Specifies the minimum peptide length for MHC class II peptides.
integer15Specifies the prediction tool(s) to use.
stringsyfpeithiSpecifies tool-specific binder thresholds in a JSON file. This can be used to override the given default binder threshold values.
stringSpecifies the affinity metric instead of the rank metric used for determining whether a peptide is considered as a binder.
booleanSpecifies whether wild-type sequences should be predicted.
booleanSpecifies that sequences of proteins, affected by provided variants, will be written to a FASTA file.
booleanWrites out supported prediction models.
booleanOptions for optimising the pipeline run execution.
Split VCF file into multiple files by number of variants.
booleanNumber of variants that should be written into one file. Default: number of variants divided by ten
integerNumber of nucleotides between previous and current variant across split.
integer110000Specifies 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.
string${projectDir}/assets/external_tools_meta.jsonSpecifies the operating system in use (Linux or Darwin). This is only necessary if conda is used.
stringlinuxTo use the ‘netmhcpan’ tool, specify the path to the original software tarball for NetMHCpan 4.0 here.
stringNoneTo use the ‘netmhc’ tool, specify the path to the original software tarball for NetMHC 4.0 here.
stringNoneTo use the ‘netmhciipan’ tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here.
stringNoneTo use the ‘netmhcii’ tool, specify the path to the original software tarball for NetMHCII 2.2 here.
stringNoneParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean