nf-core/epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
1.1.0). The latest
stable release is
3.0.0
.
Define where the pipeline should find input data and save output data.
Variants in VCF or TSV format.
stringAlleles as TXT file.
stringPeptide sequences in TSV format.
stringProtein sequences in FASTA format.
stringThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Options for the genome and proteome reference.
Specifies the human reference genome version.
stringSpecifies the reference proteome.
stringOptions for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanOptions for the peptide prediction step.
Filter against human proteome.
booleanMHC class for prediction.
integerSpecifies the maximum peptide length.
integer11Specifies the minimum peptide length.
integer8Specifies the prediction tool(s) to use.
stringsyfpeithiSpecifies whether wild-type sequences should be predicted.
booleanSpecifies that sequences of proteins, affected by provided variants, will be written to a FASTA file.
booleanWrites out supported prediction models.
booleanOptions for optimising the pipeline run execution.
Specifies the maximum number of peptide chunks.
integer100Specifies the minimum number of peptides that should be written into one chunk.
integer5000Specifies which memory mode should be used.
stringlowLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoSet 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.GBMaximum amount of time that can be requested for any single job.
string240.hParameters 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 configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string