nf-core/hic

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Name of iGenomes reference.

Path to FASTA genome file.

Full path to directory containing Bowtie index

Full path to directory containing Bwa-mem index

Hi-C processing method

Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)

Restriction motifs used during digestion. Several motifs (comma separated) can be provided.

Expected motif after DNA ligation. Several motifs (comma separated) can be provided.

Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.

Full path to restriction fragment (bed) file.

If generated by the pipeline save the annotation and indexes in the results directory.

For Hi-C protocols which are not based on enzyme digestion such as DNAse Hi-C or Micro-C

Minimum distance between loci to consider. Useful for –no-digestion mode to remove spurious ligation products. Only values > 0 are considered

Split the reads into chunks before running the pipelne

Read number per chunks if split_fastq is used

Keep aligned reads with a minimum quality value

Option for HiC-Pro end-to-end bowtie mapping

Option for HiC-Pro trimmed reads mapping

Option for Bwa-mem mapping

Save all BAM files during two-steps mapping

Keep duplicated reads

Keep multi-aligned reads

Maximum fragment size to consider. Only values > 0 are considered

Minimum fragment size to consider. Only values > 0 are considered

Maximum restriction fragment size to consider. Only values > 0 are considered

Minimum restriction fragment size to consider. Only values > 0 are considered

Update ‘pairtools parse’ options

Save a BAM file where all reads are flagged by their interaction classes

Save all types of non valid read pairs in distinct output files

Resolution to build the maps (comma separated)

Generate raw and normalized contact maps with HiC-Pro

Filter low counts rows before HiC-Pro normalization

Filter high counts rows before HiC-Pro normalization

Threshold for HiC-Pro ICE convergence

Maximum number of iteraction for HiC-Pro ICE normalization

Update ‘cooler balance’ options

Maximum resolution to build mcool file

Save raw contact maps

Minimum chromosome size to be retained. Useful for Calder2, which cannot be applied to chromosomes that do not have a sufficient number of bins.

Resolution to build count/distance plot

Define methods for TADs calling

Define methods for compartments calling

Resolution to run TADs callers (comma separated)

Resolution for compartments calling

Call chromatin loops with ‘fithichip’ (HiChIP / PLAC-seq data) and/or ‘hicexplorer’ (hicDetectLoops), comma separated. Loops are not called when unset.

This parameter must be a combination of the following values: fithichip, hicexplorer, fithichip, hicexplorer

Resolution(s) of the contact maps used for loop calling (comma separated)

BED file of 1D anchor peaks (e.g. ChIP-seq peaks of the HiChIP target) used by FitHiChIP. When unset, anchors are inferred from the valid pairs with MACS3.

Effective genome size for MACS3 peak calling: a number, scientific notation (e.g. 2.7e9 for human) or one of the MACS3 shortcuts hs, mm, ce, dm. Default: the total length of the chromosome sizes file.

This parameter must be a combination of the following values: 0, 9, 0, 9, eE, 0, 9, hs, mm, ce, dm

FitHiChIP: lower distance threshold (bp) of the interactions tested (LowDistThr)

FitHiChIP: upper distance threshold (bp) of the interactions tested (UppDistThr)

FitHiChIP: FDR threshold of the significant interactions (QVALUE)

FitHiChIP: interactions tested (IntType). 1 = peak-to-peak, 2 = peak-to-non-peak, 3 = peak-to-all, 4 = all-to-all, 5 = every type

FitHiChIP: bias regression (BiasType). Only 1 (coverage bias) is available: the ICE bias (2) runs HiC-Pro’s ice, which the FitHiChIP container does not include.

FitHiChIP: use the stringent peak-to-peak background (UseP2PBackgrnd, FitHiChIP(S)) instead of the loose background (FitHiChIP(L))

hicDetectLoops: Maximum genomic distance of a loop, usually loops are within a distance of ~2MB

hicDetectLoops: The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins

hicDetectLoops: The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins

hicDetectLoops: Only candidates with p-values less the given threshold will be considered as candidates. For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given. This does NOT influence the p-value for the neighborhood testing. Can a single value or a threshold file created by hicCreateThresholdFile

hicDetectLoops: The minimum number of interactions a detected peaks needs to have to be considered

hicDetectLoops: The minimum number of obs/exp interactions a detected peaks needs to have to be considered

hicDetectLoops: Rejection level for Anderson-Darling or Wilcoxon-rank sum test for H0. H0 is peak region and background have the same distribution

hicDetectLoops: Method to compute the expected value per distance: Either the mean (mean), the mean of non-zero values (mean_nonzero) or the mean of non-zero values with ligation factor correction (mean_nonzero_ligation)

hicPlotMatrix: transformation of the loop plot values

hicPlotMatrix: region of the loop plot, e.g. chr1:10000-20000. Whole genome when unset.

hicPlotMatrix: second region of the loop plot for inter-region contacts, used with –loop_plot_region

Do not perform FastQC

Do not build contact maps

Do not run distance/decay plot

Do not run TADs calling

Do not run compartments calling

Do not run cooler balancing normalization

Do not generate mcool file for Higlass visualization

Do not generate MultiQC report

Custom MultiQC yaml file containing HTML including a methods description.

Display the help message.

Display the full detailed help message.

Display hidden parameters in the help message (only works when –help or –help_full are provided).