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.
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 human reference genome version.
string
Specifies the reference proteome.
string
Reference genome related files and options required for the workflow.
Do not load the iGenomes reference config.
boolean
Options for the peptide prediction step.
Filter against human proteome.
boolean
Specifies the maximum peptide length.
integer
11
Specifies the minimum peptide length.
integer
8
Specifies the maximum peptide length for MHC class II peptides.
integer
16
Specifies the minimum peptide length for MHC class II peptides.
integer
15
Specifies the prediction tool(s) to use.
string
syfpeithi
Specifies tool-specific binder thresholds in a JSON file. This can be used to override the given default binder threshold values.
string
Specifies the affinity metric instead of the rank metric used for determining whether a peptide is considered as a binder.
boolean
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.
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
${projectDir}/assets/external_tools_meta.json
Specifies the operating system in use (Linux or Darwin). This is only necessary if conda is used.
string
linux
To use the ‘netmhcpan’ tool, specify the path to the original software tarball for NetMHCpan 4.0 here.
string
None
To use the ‘netmhc’ tool, specify the path to the original software tarball for NetMHC 4.0 here.
string
None
To use the ‘netmhciipan’ tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here.
string
None
To use the ‘netmhcii’ tool, specify the path to the original software tarball for NetMHCII 2.2 here.
string
None
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
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
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
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean