nf-core/hicar
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
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|tsv|yaml)$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Metho for the experiment.
stringHiCARIt can be HiCAR, HiChIP, ChIA-PET, PLAC-Seq. If it is not HiCAR, user may want to define the anchor peaks. Otherwise, the anchor peaks will be called by R2 reads.
Path to anchor peaks
string^\S+\.(narrowPeak|boradPeak)$The anchor peaks can be a narrowPeak or broadPeak.
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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
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.
Path to bwa index 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.
Path to annotation gtf file.
stringAnnotation gtf or gff file is required for annotation and quality control. This parameter is mandatory if --genome is not specified.
Path to annotation gff file.
stringAnnotation gff or gff file is required for annotation and quality control. This parameter is mandatory if --genome is not specified.
Path to annotation gene bed file.
stringPath to BED file containing gene intervals. This will be created from the GTF file if not specified.
Path to genome mappability file.
stringIf you have no genome mappability 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.
Effective genome size parameter required by MACS2.
stringEffective genome size parameter required by MACS2. If using an iGenomes reference these have been provided when --genome is set as GRCh37, GRCh38, GRCm38, WBcel235, BDGP6, R64-1-1, EF2, hg38, hg19 and mm10. For other genomes, if this parameter is not specified then the MACS2 peak-calling and differential analysis will be skipped.
Path to blacklist regions in BED format, used for filtering alignments.
stringIf provided, alignments that overlap with the regions in this file will be filtered out (see ENCODE blacklists). The file should be in BED format. Blacklisted regions for GRCh37, GRCh38, GRCm38, hg19, hg38, mm10 are bundled with the pipeline in the blacklists directory, and as such will be automatically used if any of those genomes are specified with the --genome parameter.
publish mappability to results genome/mappability folder
booleanpublish genome
booleanParameters used to describe the experiment designs.
Specifies that the cutting position has to be using.
stringCviQIDefault CviQI digestion. Available enzymes are MboI, DpnII, BglII, HindIII, MseI, and CviQI.
Specifies that the cutting sequence has to be using.
string^TACIt will be automatically assigned by the enzyme inputed.
Specifies that the cutoff value used for mappability filter.
number0.5Default is 0.5. It is the average over just covered bases.
trim 5' end with the string if not skip_cutadapt
string^TACshift size for MACS2
integer-75How reads will be shift to increase the peak/noise ratios. See help from MACS2 documentation
extsize for MACS2
integer150How reads will be extend in 5'->3' direction to increase the fragment size. See help from MACS2 documentation
cutoff qvalue
number0.01The minimum FDR cutoff to call significant peak for R2 reads. See help from MACS2 documentation
resolution bin size
string5000_10000Bin size for singal resampling.
output of restriction_cut_multipleenzyme.py.
stringNoneSee https://github.com/ijuric/MAPS/blob/master/bin/utils/genomic_features_generator/scripts/restriction_cut_multipleenzyme.py.
MAPS regression cutoff value
integer12Minimal cutoff value for coverage in the called connections. See help from MAPS documentation, default 12.
MAPS regression fold change cutoff value
number2Miniaml cutoff value for fold change from signal to expected values. See help from MAPS documentation, default 2.
MAPS regression -log10(fdr) cutoff value
number2Minimal cutoff -log10(FDR) value in the called connections. See help from MAPS documentation, default 2 (=fdr 0.01).
MAPS regression filter file name
stringNonefile containing bins that need to be filtered out. Format: two columns 'chrom', 'bin'. 'chrom' contains 'chr1','chr2',.. 'bin' is bin label
MAPS regression type
stringpospoisson for positive poisson regression, negbinom for negative binomial. default is pospoisson.
remove duplicates for high resolution peaks or not
booleanType of snow cluster to use
stringSOCKPossible values are 'SOCK' (default), 'MPI' and 'FORK'. This will be used by snow package for HiPeak calling
The block number of peak pair
number1000000000The block number of peak pair in each thread to count the reads. Smaller number will decrease the memory cost and increase the computation time for parepare the counts in hipeak calling.
The minimal number reads count of peak pair
integer1create cooler files for MAPS or not
booleanFDR cutoff value
number0.05Minimal cutoff FDR value in the called connections. See help from HiCDCPlus documentation, default 0.05.
The predefined modle download prefix string
stringhttp://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained.This method is only available for HiCAR data.
Call high resolution peaks or not
booleancutoff pvalue for fragment (R1)
number0.1The minimum FDR cutoff to call significant peak for R1 reads. R1 reads will be more noisy compare to R2 reads. Here we need a loose cutoff. And this will be fixed in the following steps.
The resolution for compartments calling
integer100000The resolution for TADs calling
integer10000If tad_tool is set to resolution, the windows will be calculated by 3X, 5X, 10X and 15X resolution. If tad_tool is set to hicfindtads, this will determine the step parameter.
The caller for TADs, available choices: 'cooltools', 'hicexplorer', 'homer'
stringPossible tools are hicfindtads and cooltools (by insulation function).
The APA peak path
stringAnchor 1D peaksAPA tool, available choices: 'cooltools', 'hicexplorer', and 'juicebox'
stringThe APA output figure format. Currently this parameter will not affect the Juicer output format (always png format).
stringpngCall compartment tool, available choices: 'cooltools', 'hicexplorer', 'homer', and 'juicebox'
stringCall loops tool, available choices: 'maps', 'hicdcplus', and 'peakachu'
stringDifferential analysis tool. Possible options are 'edger', 'diffhic', 'hicexplorer', and 'setOperation'
stringvirtual 4c tool, available choices: 'cooltools', 'hicexplorer', and 'trackviewer'
stringTranscription Factor Enrichment Analysis tool, available choices: 'atacseqtfea', and 'homer'
stringjuicer_tools jar file url
stringhttps://github.com/aidenlab/JuicerTools/releases/download/v3.0.0/juicer_tools.3.0.0.jarThe juicer_tools is ued for downstream analysis such as apa/arrowhead/hiccups. The juicer_tools can be downloaded from juicer_tools download page
Normalization methods
stringSee more details at addNorm. Avaiable selection are limited by APA and Eigenvector normalization methods.
parameter for HiCExplorer ChicSignificantinterations
integer2extension file name for MAPS
stringsig3Dinteractions.pe.txtextension file name for long pairs
stringlong.bedpeextension file name for short pairs
stringshrt.vip.bedOptions for tracks viewed by igv, ucsc genome browser and virtual 4c plot tools
max events to plot for virtual 4c
integer25The HiCTools path
stringhttps://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jarThis tool is used for pre/addNorm/eigenvector/pearsons/sum. Pre is the tool to create .hic file; eigenvector is used for compartment caller. The hic_tools can be downloaded from HiCTools download page
skip peak QC or not
booleanskip plot profile or not
booleanskip creat IGV files or not
booleanskip create trackhub files or not
booleancutoff value for false discovery rate of enrichment analysis
numberParameters 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.
To skip some processes or workflows.
skip trim 5'end
booleanresample the pairs by pairtools
booleanskip fastqc or not
booleanskip peak annotation or not
booleanskip differential analysis or not
booleanskip multiqc or not
booleanrun APA or not
booleanskip call compartment or not
booleanskip call TADs or not
booleanskip call interactions/loops
booleanDo Transcription Factor Enrichment Analysis or not
booleancreate track files for virtual 4c or not
booleanskip circos plot
boolean