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.
3.0). 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$The output directory where the results will be saved. You have to use absolute paths to store on Cloud infrastructure.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSave genome reference data to the output directory
booleanSave any technical replicate FASTQ files that were merged to the output directory
booleanSave trimmed FASTQ files to the output directory
booleanSave BAM files aligned to the spike-in genome to the output directory
booleanSave unaligned sequences to the output directory
booleanSave alignment intermediates to the output directory (WARNING: can be very large)
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Reference genome related files and options.
Name of iGenomes reference.
stringPath 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
stringK12-MG1655Path to spike-in bowtie2 index
stringPath to spike-in fasta
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanRun 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.
integerSelect aligner
stringbowtie2Normalisation constant for spike-in read normalisation
integer10000Filter reads below a q-score threshold
integerDe-duplicate target reads AND control reads (default is control only)
booleanSets 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.
integer1Selects 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 p-value threshold for peaks
number0.05SEACR normalization.
stringSEACR stringency.
stringP-value threshold for macs2 peak caller
number0.05parameter 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 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)
integer3000Minimum fragment overlap for FriP score
number0.2Minimum peak overlap for peak reproducibility plot
number0.2Parameters 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 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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${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.
boolean