nf-core/cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
1.1). The latest
stable release is
3.2.2
.
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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Path to the output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSave reference data to output directory
booleanSave any technical replicates that were merged to output directory
booleanSave trimmed fastqs to output directory
booleanSave bam files aligned to the spike-in genome to output directory
booleanSave unaligned sequences to output directory
booleanSave alignment intermediates to output directory (WARNING: can be very large)
booleanSelect aligner
stringbowtie2Trim galore param
integerTrim galore param
integerTrim galore param
integerTrim galore param
integerTrim galore param
integerReference genome related files and options required for the workflow.
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 bowtie2 index
stringPath to GTF annotation file
stringPath to genome blacklist
stringName of the igenome reference for the spike-in genome
stringK12-MG1655Path to spike-in bowtie2 index
stringPath to spike-in fasta
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo 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.
Filter reads below a q-score threshold
integerDeduplicate non-control reads
booleanNormalisation constant
integer10000Specifies if the samplesheet contains an IgG control
booleantrueThreshold for peak calling when no IgG is present
number0.05Path to gene bed file
stringMinimum number of overlapping replicates needed for a consensus peak
integer1Run pipeline up to reference preparation
booleanRun pipeline up to input checking
booleanRun pipeline up to pre-alignment
booleanRun pipeline up to alignment
booleanRun pipeline up to q-filtering
booleanRun pipeline up to peak calling
booleanSkips fastqc reporting
booleanSkips trimming
booleanSkips de-duplication
booleanSkips scalefactor normalisation
booleanSkips reporting
booleanSkips igv session generation
booleanSkips deeptools heatmaps
booleanSkips multiqc
booleanSkip upset plot calculation
booleanParameters 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/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 this parameter.
Institutional 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.
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.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use 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.h^(\d+\.?\s*(s|m|h|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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.
booleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
booleanThis may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues.