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.
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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to store on Cloud infrastructure.
string./resultsMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSave genome reference data to the output directory
booleanSave any technical replicate FASTQ files that were merged to the output directory
booleanSave trimmed FASTQ files to the output directory
booleanSave BAM files aligned to the spike-in genome to the output directory
booleanSave unaligned sequences to the output directory
booleanSave alignment intermediates to the output directory (WARNING: can be very large)
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
Output calculated scale factors from pipeline
booleanReference genome related files and options.
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 gene BED file
stringPath to genome blacklist
stringName of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6
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.
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.
Run pipeline up to input checking
booleanRun pipeline up to reference preparation
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 reporting
booleanSkips preseq reporting
booleanSkips igv session generation
booleanSkips deeptools QC repoting
booleanSkips deeptools heatmap generation
booleanSkips peak QC reporting
booleanSkips multiqc
booleanInstructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
integerInstructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
integerInstructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.
integerThis enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.
Select aligner
stringbowtie2Normalisation constant for spike-in read normalisation
integer10000Filter reads below a q-score threshold
integer20Filter mitochondrial reads
booleanName of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome.
stringDe-duplicate target reads AND control reads (default is control only)
booleanDe-duplicate reads based on read 1 5' start position. Relevant for assays using linear amplification with tagmentation (default is false).
booleanUse --end-to-end mode of Bowtie2 during alignment
booleantrueSets the target read normalisation mode. Options are: ["Spikein", "RPKM", "CPM", "BPM", "None" ]
stringIf normsalisation option is one of "RPKM", "CPM", "BPM" - then the binsize that the reads count is calculated on is used.
integer50Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary peak callers will be run and outputed to the results folder.
stringseacrSpecifies whether to use a control to normalise peak calls against (e.g. IgG)
booleantrueSpecifies whether to extend paired-end fragments between the read mates when calculating coveage tracks
booleantrueSpecifies whether the background control is scaled prior to being used to normalise peaks.
number0.5SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if --use_control is false
number0.05SEACR normalization.
stringSEACR stringency.
stringQ-value threshold for MACS2 peak caller.
number0.01P-value threshold for macs2 peak caller. If set it will overide the qvalue.
numberparameter required by MACS2. If using an iGenomes reference these have been provided when --genome is set as GRCh37, GRCh38, GRCm38, WBcel235, BDGP6, R64-1-1, EF2, hg38, hg19 and mm10. Otherwise the gsize will default to GRCh38.
number2700000000Determines whether MACS2 broad or narrow peak mode is used for the peak caller
booleantrueMACS2 broad cutoff parameter
number0.1Specifies what samples to group together for consensus peaks. Options are [group, all]
stringMinimum number of overlapping replicates needed for a consensus peak
number1Show gene names instead of symbols in IGV browser sessions
booleantrueDeeptools multiBamSummary bam bin size
integer500Deeptools Correlation Plot statistical calculation method
stringpearsonDeeptools heatmap gene plot before length (bases)
integer3000Deeptools heatmap gene plot body length (bases)
integer5000Deeptools heatmap gene plot after length (bases)
integer3000Deeptools heatmap peak plot before length (bases)
integer3000Deeptools heatmap peak plot after length (bases)
integer3000Flag for whether to generate a heatmap for all samples together
booleantrueMinimum fragment overlap for FriP score
number0.2Minimum peak overlap for peak reproducibility plot
number0.2Sort the IGV output tracks by group
booleantrueParameters 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|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Pull Docker container.
booleanEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.