nf-core/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
1.3.0). The latest
stable release is
2.1.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files.
stringUse this to specify the location of your input FastQ files. For example:
--input 'path/to/data/sample_*_{1,2}.fastq'
Please note the following requirements:
- The path must be enclosed in quotes
- The path must have at least one
*wildcard character - When using the pipeline with paired end data, the path must use
{1,2}notation to specify read pairs.
If left unspecified, a default pattern is used: data/*{1,2}.fastq.gz
Input FastQ files for test only
stringundefinedThe output directory where the results will be saved.
string./resultsEmail 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.
Options for the reference genome indices used to align reads.
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.
stringIf you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo 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 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
stringhindiiiRestriction motifs used during digestion. Several motifs (comma separated) can be provided.
string'A^AGCTT'Expected motif after DNA ligation. Several motifs (comma separated) can be provided.
string'AAGCTAGCTTFull 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.
Save the non valid pairs detected by HiC-Pro.
booleanUse this parameter to save non valid pairs detected by HiC-Pro (dangling-end, self-circle, re-ligation, filtered).
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 -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
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
string5000Set 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+)*$Skip some steps of the pipeline
Do not build contact maps
booleanDo not run distance/decay plot
booleanDo not run TADs calling
booleanDo not run compartments calling
stringDo not run cooler balancing normalization
booleanDo not generate mcool file for Higlass visualization
booleanDo not generate MultiQC report
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Boolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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|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'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config name
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string