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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?s?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have an index available this will be generated for you automatically. Combine with --save_reference to save the mapping index for future runs.
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.
Full path to directory containing Bowtie index
stringFull path to directory containing Bwa-mem index
stringDefine the Hi-C processing subworkflow to use to extract the valid pairs from raw data
Hi-C processing method
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)`.
stringIf not specified, the pipeline will build this file from the reference genome file
Full path to restriction fragment (bed) file.
stringThis file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option
If generated by the pipeline save the annotation and indexes in the results directory.
booleanUse this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.
Parameters 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 --end-to-end --reorderOption for HiC-Pro trimmed reads mapping
string--very-sensitive --end-to-end --reorderOption for Bwa-mem mapping
string-5SP -T0Save 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
integerUpdate 'pairtools parse' options
string--walks-policy 5uniqueSave 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^(\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
integer100Update 'cooler balance' options
string--forceMaximum resolution to build mcool file
stringSave raw contact maps
booleanSet up downstream analysis from contact maps
Resolution to build count/distance plot
string250000^(\d+)(,\d+)*$Define methods for TADs calling
stringinsulationResolution to run TADs callers (comma separated)
string40000^(\d+)(,\d+)*$Resolution for compartments calling
string250000^(\d+)(,\d+)*$Skip some steps of the pipeline
Do not build contact maps
booleanDo not run distance/decay plot
booleanDo not run TADs calling
booleanDo not run compartments calling
booleanDo not run cooler balancing normalization
booleanDo not generate mcool file for Higlass visualization
booleanDo not generate MultiQC report
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/