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.
string
Alleles as TXT file.
string
Peptide sequences in TSV format.
string
Protein sequences in FASTA format.
string
The output directory where the results will be saved.
string
./results
Email 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.
string
Specifies the reference proteome.
string
Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
Options for the peptide prediction step.
Filter against human proteome.
boolean
MHC class for prediction.
integer
Specifies the maximum peptide length.
integer
11
Specifies the minimum peptide length.
integer
8
Specifies the prediction tool(s) to use.
string
syfpeithi
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
Writes out supported prediction models.
boolean
Options for optimising the pipeline run execution.
Specifies the maximum number of peptide chunks.
integer
100
Specifies the minimum number of peptides that should be written into one chunk.
integer
5000
Specifies which memory mode should be used.
string
low
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Workflow name.
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
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
Maximum amount of time that can be requested for any single job.
string
240.h
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 configs hostname.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string