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.
string
Email 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.
string
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?s?a(sta)?(\.gz)?$
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Full path to directory containing Bowtie index
string
Full path to directory containing Bwa-mem index
string
Define the Hi-C processing subworkflow to use to extract the valid pairs from raw data
Hi-C processing method
string
Parameters for protocols based on restriction enzyme
Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)
string
Restriction motifs used during digestion. Several motifs (comma separated) can be provided.
string
Expected motif after DNA ligation. Several motifs (comma separated) can be provided.
string
Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.
string
Full path to restriction fragment (bed) file.
string
If generated by the pipeline save the annotation and indexes in the results directory.
boolean
Parameters for protocols which are not based on restriction enzymes
For Hi-C protocols which are not based on enzyme digestion such as DNAse Hi-C or Micro-C
boolean
Minimum distance between loci to consider. Useful for —no-digestion mode to remove spurious ligation products. Only values > 0 are considered
integer
Parameters for reads aligments
Split the reads into chunks before running the pipelne
boolean
Read number per chunks if split_fastq is used
integer
20000000
Keep aligned reads with a minimum quality value
integer
10
Option for HiC-Pro end-to-end bowtie mapping
string
--very-sensitive --end-to-end --reorder
Option for HiC-Pro trimmed reads mapping
string
--very-sensitive --end-to-end --reorder
Option for Bwa-mem mapping
string
-5SP -T0
Save all BAM files during two-steps mapping
boolean
Options to call significant interactions
Keep duplicated reads
boolean
Keep multi-aligned reads
boolean
Maximum fragment size to consider. Only values > 0 are considered
integer
Minimum fragment size to consider. Only values > 0 are considered
integer
Maximum restriction fragment size to consider. Only values > 0 are considered
integer
Minimum restriction fragment size to consider. Only values > 0 are considered
integer
Update ‘pairtools parse’ options
string
--walks-policy 5unique
Save a BAM file where all reads are flagged by their interaction classes
boolean
Save all types of non valid read pairs in distinct output files
boolean
Options to build Hi-C contact maps
Resolution to build the maps (comma separated)
string
1000000
^(\d+)(,\d+)*$
Generate raw and normalized contact maps with HiC-Pro
boolean
Filter low counts rows before HiC-Pro normalization
number
0.02
Filter high counts rows before HiC-Pro normalization
integer
Threshold for HiC-Pro ICE convergence
number
0.1
Maximum number of iteraction for HiC-Pro ICE normalization
integer
100
Update ‘cooler balance’ options
string
--force
Maximum resolution to build mcool file
string
Save raw contact maps
boolean
Set up downstream analysis from contact maps
Resolution to build count/distance plot
string
250000
^(\d+)(,\d+)*$
Define methods for TADs calling
string
insulation
Define methods for compartments calling
string
cooltools
Resolution to run TADs callers (comma separated)
string
40000
^(\d+)(,\d+)*$
Resolution for compartments calling
string
250000
^(\d+)(,\d+)*$
Skip some steps of the pipeline
Do not build contact maps
boolean
Do not run distance/decay plot
boolean
Do not run TADs calling
boolean
Do not run compartments calling
boolean
Do not run cooler balancing normalization
boolean
Do not generate mcool file for Higlass visualization
boolean
Do not generate MultiQC report
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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.
string