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)$Metho for the experiment.
stringHiCARPath to anchor peaks
string^\S+\.(narrowPeak|boradPeak)$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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanPath to bwa index file.
stringPath to annotation gtf file.
stringPath to annotation gff file.
stringPath to annotation gene bed file.
stringPath to genome mappability file.
stringEffective genome size parameter required by MACS2.
stringUCSC assembly annotation name.
stringPath to blacklist regions in BED format, used for filtering alignments.
stringpublish mappability to results genome/mappability folder
booleanpublish genome
booleanParameters used to describe the experiment designs.
Specifies that the cutting position has to be using.
stringCviQISpecifies that the cutting sequence has to be using.
string^TACSpecifies that the cutoff value used for mappability filter.
number0.5trim 5’ end with the string if not skip_cutadapt
string^TACshift size for MACS2
integer-75extsize for MACS2
integer150cutoff qvalue
number0.01resolution bin size
string5000_10000output of restriction_cut_multipleenzyme.py.
stringNoneMAPS regression cutoff value
integer12MAPS regression fold change cutoff value
number2MAPS regression -log10(fdr) cutoff value
number2MAPS regression filter file name
stringNoneMAPS regression type
stringremove duplicates for high resolution peaks or not
booleanType of snow cluster to use
stringSOCKThe block number of peak pair
number1000000000The minimal number reads count of peak pair
integer1create cooler files for MAPS or not
booleanFDR cutoff value
number0.05The predefined modle download prefix string
stringhttp://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained.Call high resolution peaks or not
booleancutoff pvalue for fragment (R1)
number0.1The resolution for compartments calling
integer100000The resolution for TADs calling
integer10000The caller for TADs, available choices: ‘cooltools’, ‘hicexplorer’, ‘homer’
stringThe 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.jarNormalization methods
stringparameter 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.jarskip 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/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$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$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.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
booleanTo 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