nf-core/epigenomesegmentation
An nf-core pipeline for epigenome segmentation using EpiSegMix/Meth — a hidden Markov model with flexible read count distributions and state duration modeling for histone, open chromatin, and methylation signals.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters specific to the EpiSegMix algorithm configuration.
Run the standard HMM model (default).
booleanRun the duration HMM (DM) model to account for segment length.
booleanRun the DNA methylation mode.
booleanRun the distribution fitting mode to find optimal statistical distributions.
booleanRun only count generation (skip all downstream analysis).
booleanAutomatically run standard segmentation using the best-fit distributions after ‘fitting’ mode completes.
booleanComma-separated list of statistical distributions to test during ‘fitting’ mode (e.g., ‘NBI,P,ZINB’).
stringNBI,SI,BNBGenomic bin size in base pairs used for discretising the genome.
integer200Number of chromatin states in the HMM model.
integer,string8Merge adjacent segments with the same chromatin state label.
booleanDecoding algorithm for inferring the most likely chromatin state sequence.
stringAdjustment parameter for emission probability smoothing.
integer2Maximum number of iterations for model training.
integer200Convergence threshold for the algorithm.
number1Chromosome used for initial parameter estimation. Specify by index or name.
string,integer12Default distribution model for histone modification counts if not specified in the samplesheet (e.g. NBI for negative binomial).
stringNBIDefault distribution model for DNA methylation levels if not specified in the samplesheet (e.g. BI for beta-binomial).
stringBIReference genome related files and options required for the workflow.
Name of reference genome.
stringhg38Parameters 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.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
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.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when —help or —help_full are provided).
boolean