nf-core/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
1.2.2). The latest
stable release is
2.1.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files.
stringInput FastQ files for test only
stringundefinedSplit the reads into chunks before running the pipelne
booleanfalseRead number per chunks if split_fastq is used
integer20000000Specifies that the input is single-end reads.
booleanThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Options for the reference genome indices used to align reads.
Name of iGenomes reference.
stringPath to FASTA genome file.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanFull path to directory containing Bowtie index including base name. i.e. /path/to/index/base.
stringFull path to file specifying chromosome sizes (tab separated with chromosome name and size)`.
stringFull path to restriction fragment (bed) file.
stringIf generated by the pipeline save the annotation and indexes in the results directory.
booleanParameters for Hi-C data processing
For Hi-C protocols which are not based on enzyme digestion such as DNase Hi-C
booleanRestriction motifs used during digestion. Several motifs (comma separated) can be provided.
string'A^AGCTT'Expected motif after DNA ligation. Several motifs (comma separated) can be provided.
string'AAGCTAGCTTRemove duplicates
booleantrueRemove multi-mapped reads
booleantrueRemove singleton
booleantrueKeep aligned reads with a minimum quality value
integer10Option for end-to-end bowtie mapping
string'--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'Option for trimmed reads mapping
string'--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'Save a BAM file where all reads are flagged by their interaction classes
booleanSave all BAM files during two-steps mapping
booleanOptions to call significant interactions
Minimum distance between loci to consider. Useful for —dnase mode to remove spurious ligation products. Only values > 0 are considered
integerOMaximum fragment size to consider. Only values > 0 are considered
integer0Minimum fragment size to consider. Only values > 0 are considered
integer0Maximum restriction fragment size to consider. Only values > 0 are considered
integer0Minimum restriction fragment size to consider. Only values > 0 are considered
integer0Options to build Hi-C contact maps
Resolution to build the maps (comma separated)
string'1000000,500000'Filter low counts rows before normalization
string0.02Filter high counts rows before normalization
integer0Threshold for ICE convergence
string0.1Maximum number of iteraction for ICE normalization
integer100Skip some steps of the pipeline
Do not build contact maps
booleanDo not normalize contact maps
booleanDo not generate cooler file
booleanDo not generate MultiQC report
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
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.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoSet 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.GBMaximum amount of time that can be requested for any single job.
string240.hParameters 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 configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string