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.
stringUse this to specify the location of your input FastQ files. For example:
--input 'path/to/data/sample_*_{1,2}.fastq'
Please note the following requirements:
- The path must be enclosed in quotes
- The path must have at least one
*wildcard character - When using the pipeline with paired end data, the path must use
{1,2}notation to specify read pairs.
If left unspecified, a default pattern is used: data/*{1,2}.fastq.gz
Input 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.
booleanBy default, the pipeline expects paired-end data. If you have single-end data, you need to specify --single_end on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for --input. For example:
--single_end --input '*.fastq'
It is not possible to run a mixture of single-end and paired-end files in one run.
The 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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Options for the reference genome indices used to align reads.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
stringIf you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Full 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)`.
stringIf not specified, the pipeline will build this file from the reference genome file
Full path to restriction fragment (bed) file.
stringThis file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option
If generated by the pipeline save the annotation and indexes in the results directory.
booleanUse this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.
Parameters 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.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Workflow name.
stringA custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom 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.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GBUse to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.hUse to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string