nf-core/epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
2.3.0). The latest
stable release is
2.3.1
.
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.
stringYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for the genome and proteome reference.
Specifies the Ensembl genome reference version that will be used.
stringgrch37This defines against which human Ensembl genome reference the pipeline performs the analysis including the incorporation of genetic variants. If grch37 or grch38 are specified, the most recent Ensembl Biomart version for genome versions will be used. Alternatively, an Ensembl Biomart (archive) version can be specified, e.g. http://jan2020.archive.ensembl.org/.
Specifies the reference proteome.
stringSpecifies the reference proteome files that are used for self-filtering. Should be either a folder of FASTA files or a single FASTA file containing the reference proteome(s).
Reference genome related files and options required for the workflow.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Options for the peptide prediction step.
Filter against human proteome.
booleanSpecifies that peptides should be filtered against the specified human proteome references.
Specifies the maximum peptide length.
integer11Specifies the maximum peptide length (not applied when --peptides is specified). Default: MHC class I: 11 aa, MHC class II: 16 aa
Specifies the minimum peptide length.
integer8Specifies the minimum peptide length (not applied when --peptides is specified). Default: MCH class I: 8 aa, MHC class II: 15 aa
Specifies 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 the tool(s) to use. Multiple tools can be combined in a list separated by comma.
Available are: syfpeithi, mhcflurry, mhcnuggets-class-1, mhcnuggets-class-2,netmhcpan-4.0,netmhcpan-4.1,netmhc-4.0,netmhciipan-4.1.
syfpeithi, mhcnuggets, class, 1, mhcnuggets, class, 2, mhcflurry, netmhc, 4, 0, netmhcpan, 4, 0, netmhcpan, 4, 1, netmhciipan, 4, 1, netmhc_darwin, 4, 0, netmhcpan_darwin, 4, 0, netmhcpan_darwin, 4, 1, netmhciipan_darwin, 4, 1, syfpeithi, mhcnuggets, class, 1, mhcnuggets, class, 2, mhcflurry, netmhc, 4, 0, netmhcpan, 4, 0, netmhcpan, 4, 1, netmhciipan, 4, 1, netmhc_darwin, 4, 0, netmhcpan_darwin, 4, 0, netmhcpan_darwin, 4, 1, netmhciipan_darwin, 4, 1Specifies tool-specific binder thresholds in a JSON file. This can be used to override the given default binder threshold values.
stringDefault thresholds to determine whether a peptide is considered as a binder are the following: syfpeithi > 50, mhcflurry <=500, mhcnuggets-class-1 <= 500, mhcnuggets-class-2 <= 500, netmhc <= 2, netmhcpan <= 2, netmhcii <= 5, netmhciipan <= 5. Note that the default threshold for NetMHC tools is based on the rank metric. The remaining predictors thresholds are based on affinities. Thresholds can be customized in a JSON file: tool-name:value
Specifies the affinity metric instead of the rank metric used for determining whether a peptide is considered as a binder.
booleanSwitches the prediction metric of netMHC tools from rank to affinity. Default: netmhc <= 500, netmhcpan <= 500, netmhcii <= 500, netmhciipan <= 500.
Specifies whether wild-type sequences should be predicted.
booleanSpecifies whether wild-type sequences of mutated peptides should be predicted as well.
Specifies that sequences of proteins, affected by provided variants, will be written to a FASTA file.
booleanSpecifies that sequences of proteins that are affected by the provided genomic variants are written to a FASTA file. The resulting FASTA file will contain the wild-type and mutated protein sequences.
Writes out supported prediction models.
booleanWrites out supported models. Does not run any predictions.
Options 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.
integer110000This can be used to avoid that variants end up in separate splits that fall onto the same transcript and therefore potentially contribute to the same mutated protein.
Specifies the maximum number of peptide chunks.
integer100Used in combination with --peptides or --proteins. Maximum number of peptide chunks that will be created for parallelisation.
Specifies the minimum number of peptides that should be written into one chunk.
integer5000Used in combination with --peptides or --proteins: minimum number of peptides that should be written into one chunk.
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.
stringSpecifies the operating system in use (Linux or Darwin). This is only necessary if conda is used.
stringTo use the 'netmhcpan' tool, specify the path to the original software tarball for NetMHCpan 4.0 here.
string^\S+\.tar\.gz$To use the 'netmhc' tool, specify the path to the original software tarball for NetMHC 4.0 here.
string^\S+\.tar\.gz$To use the 'netmhciipan' tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here.
string^\S+\.tar\.gz$To use the 'netmhcii' tool, specify the path to the original software tarball for NetMHCII 2.2 here.
string^\S+\.tar\.gz$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Show all params when using --help
boolean