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.
string
HiCAR
Path 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.
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?a(sta)?(\.gz)?$
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Path to bwa index file.
string
Path to annotation gtf file.
string
Path to annotation gff file.
string
Path to annotation gene bed file.
string
Path to genome mappability file.
string
Effective genome size parameter required by MACS2.
string
UCSC assembly annotation name.
string
Path to blacklist regions in BED format, used for filtering alignments.
string
publish mappability to results genome/mappability folder
boolean
publish genome
boolean
Parameters used to describe the experiment designs.
Specifies that the cutting position has to be using.
string
CviQI
Specifies that the cutting sequence has to be using.
string
^TAC
Specifies that the cutoff value used for mappability filter.
number
0.5
trim 5’ end with the string if not skip_cutadapt
string
^TAC
shift size for MACS2
integer
-75
extsize for MACS2
integer
150
cutoff qvalue
number
0.01
resolution bin size
string
5000_10000
output of restriction_cut_multipleenzyme.py.
string
None
MAPS regression cutoff value
integer
12
MAPS regression fold change cutoff value
number
2
MAPS regression -log10(fdr) cutoff value
number
2
MAPS regression filter file name
string
None
MAPS regression type
string
remove duplicates for high resolution peaks or not
boolean
Type of snow cluster to use
string
SOCK
The block number of peak pair
number
1000000000
The minimal number reads count of peak pair
integer
1
create cooler files for MAPS or not
boolean
FDR cutoff value
number
0.05
The predefined modle download prefix string
string
http://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained.
Call high resolution peaks or not
boolean
cutoff pvalue for fragment (R1)
number
0.1
The resolution for compartments calling
integer
100000
The resolution for TADs calling
integer
10000
The caller for TADs, available choices: ‘cooltools’, ‘hicexplorer’, ‘homer’
string
The APA peak path
string
Anchor 1D peaks
APA tool, available choices: ‘cooltools’, ‘hicexplorer’, and ‘juicebox’
string
The APA output figure format. Currently this parameter will not affect the Juicer output format (always png format).
string
png
Call compartment tool, available choices: ‘cooltools’, ‘hicexplorer’, ‘homer’, and ‘juicebox’
string
Call loops tool, available choices: ‘maps’, ‘hicdcplus’, and ‘peakachu’
string
Differential analysis tool. Possible options are ‘edger’, ‘diffhic’, ‘hicexplorer’, and ‘setOperation’
string
virtual 4c tool, available choices: ‘cooltools’, ‘hicexplorer’, and ‘trackviewer’
string
Transcription Factor Enrichment Analysis tool, available choices: ‘atacseqtfea’, and ‘homer’
string
juicer_tools jar file url
string
https://github.com/aidenlab/JuicerTools/releases/download/v3.0.0/juicer_tools.3.0.0.jar
Normalization methods
string
parameter for HiCExplorer ChicSignificantinterations
integer
2
extension file name for MAPS
string
sig3Dinteractions.pe.txt
extension file name for long pairs
string
long.bedpe
extension file name for short pairs
string
shrt.vip.bed
Options for tracks viewed by igv, ucsc genome browser and virtual 4c plot tools
max events to plot for virtual 4c
integer
25
The HiCTools path
string
https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar
skip peak QC or not
boolean
skip plot profile or not
boolean
skip creat IGV files or not
boolean
skip create trackhub files or not
boolean
cutoff value for false discovery rate of enrichment analysis
number
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
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
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
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean
To skip some processes or workflows.
skip trim 5’end
boolean
resample the pairs by pairtools
boolean
skip fastqc or not
boolean
skip peak annotation or not
boolean
skip differential analysis or not
boolean
skip multiqc or not
boolean
run APA or not
boolean
skip call compartment or not
boolean
skip call TADs or not
boolean
skip call interactions/loops
boolean
Do Transcription Factor Enrichment Analysis or not
boolean
create track files for virtual 4c or not
boolean
skip circos plot
boolean