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.
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
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
shift size for MACS2
integer
-75
extsize for MACS2
integer
150
cutoff qvalue
number
0.01
read peak calling for fragment (R1) reads by MACS2
boolean
cutoff pvalue for fragment (R1)
number
0.1
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
source code path for merge_map.py
string
https://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/merge_map.py
feature_frag2bin source path
string
https://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/feature_frag2bin.py
make_maps_runfile source path
string
https://raw.githubusercontent.com/ijuric/MAPS/18c1a337f222130d7c5735d051614e2a253d5319/bin/MAPS/make_maps_runfile.py
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
Options for tracks viewed by igv, ucsc genome browser and virtual 4c plot tools
create track files for virtual 4c or not
boolean
max events to plot for virtual 4c
integer
25
JVM heap parameters for juicer
string
-Xms512m -Xmx4096m
The juicer_tools path
string
https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicer/juicer_tools_1.22.01.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|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
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
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean
To skip some processes or workflows.
skip trim 5’end TAC
boolean
skip fastqc or not
boolean
skip peak annotation or not
boolean
skip enrichment or not
boolean
true
skip differential analysis or not
boolean
skip multiqc or not
boolean