nf-core/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?s?a(sta)?(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanFull path to directory containing Bowtie index including base name. i.e. /path/to/index/base.
stringParameters for protocols based on restriction enzyme
Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)
stringRestriction motifs used during digestion. Several motifs (comma separated) can be provided.
stringExpected motif after DNA ligation. Several motifs (comma separated) can be provided.
stringFull path to file specifying chromosome sizes (tab separated with chromosome name and size)`.
stringFull path to restriction fragment (bed) file.
stringIf generated by the pipeline save the annotation and indexes in the results directory.
booleanParameters for protocols based on DNAse digestion
For Hi-C protocols which are not based on enzyme digestion such as DNase Hi-C
booleanMinimum distance between loci to consider. Useful for —dnase mode to remove spurious ligation products. Only values > 0 are considered
integerParameters for reads aligments
Split the reads into chunks before running the pipelne
booleanRead number per chunks if split_fastq is used
integer20000000Keep aligned reads with a minimum quality value
integer10Option for HiC-Pro end-to-end bowtie mapping
string'--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'Option for HiC-Pro trimmed reads mapping
string'--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'Save all BAM files during two-steps mapping
booleanOptions to call significant interactions
Keep duplicated reads
booleanKeep multi-aligned reads
booleanMaximum fragment size to consider. Only values > 0 are considered
integerMinimum fragment size to consider. Only values > 0 are considered
integerMaximum restriction fragment size to consider. Only values > 0 are considered
integerMinimum restriction fragment size to consider. Only values > 0 are considered
integerSave a BAM file where all reads are flagged by their interaction classes
booleanSave all types of non valid read pairs in distinct output files
booleanOptions to build Hi-C contact maps
Resolution to build the maps (comma separated)
string1000000,500000^(\d+)(,\d+)*$Generate raw and normalized contact maps with HiC-Pro
booleanFilter low counts rows before HiC-Pro normalization
number0.02Filter high counts rows before HiC-Pro normalization
integerThreshold for HiC-Pro ICE convergence
number0.1Maximum number of iteraction for HiC-Pro ICE normalization
integer100Maximum resolution to build mcool file
string5000Save raw contact maps
booleanSet up downstream analysis from contact maps
Resolution to build count/distance plot
string1000000^(\d+)(,\d+)*$Define methods for TADs calling
stringhicexplorer,insulationResolution to run TADs callers (comma separated)
string40000,20000^(\d+)(,\d+)*$Resolution for compartments calling
string250000^(\d+)(,\d+)*$Skip some steps of the pipeline
Do not build contact maps
booleanDo not run distance/decay plot
booleanDo not run TADs calling
booleanDo not run compartments calling
booleanDo not run cooler balancing normalization
booleanDo not generate mcool file for Higlass visualization
booleanDo not generate MultiQC report
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
boolean