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$Metho for the experiment.
stringHiCARPath to anchor peaks
string^\S+\.(narrowPeak|boradPeak)$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.
stringParameters 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.
number0.5shift size for MACS2
integer-75extsize for MACS2
integer150cutoff qvalue
number0.01read peak calling for fragment (R1) reads by MACS2
booleancutoff pvalue for fragment (R1)
number0.1resolution 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
stringsource code path for merge_map.py
stringhttps://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/merge_map.pyfeature_frag2bin source path
stringhttps://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/feature_frag2bin.pymake_maps_runfile source path
stringhttps://raw.githubusercontent.com/ijuric/MAPS/18c1a337f222130d7c5735d051614e2a253d5319/bin/MAPS/make_maps_runfile.pyremove duplicates for high resolution peaks or not
booleanType of snow cluster to use
stringSOCKThe block number of peak pair
number1000000000Options for tracks viewed by igv, ucsc genome browser and virtual 4c plot tools
create track files for virtual 4c or not
booleanmax events to plot for virtual 4c
integer25JVM heap parameters for juicer
string-Xms512m -Xmx4096mThe juicer_tools path
stringhttps://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicer/juicer_tools_1.22.01.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$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
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.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanTo skip some processes or workflows.
skip trim 5’end TAC
booleanskip fastqc or not
booleanskip peak annotation or not
booleanskip enrichment or not
booleantrueskip differential analysis or not
booleanskip multiqc or not
boolean