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$
The output directory where the results will be saved. You have to use absolute paths to store on Cloud infrastructure.
string
./results
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Save genome reference data to the output directory
boolean
Save any technical replicate FASTQ files that were merged to the output directory
boolean
Save trimmed FASTQ files to the output directory
boolean
Save BAM files aligned to the spike-in genome to the output directory
boolean
Save unaligned sequences to the output directory
boolean
Save alignment intermediates to the output directory (WARNING: can be very large)
boolean
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Output calculated scale factors from pipeline
boolean
Reference genome related files and options.
Name of iGenomes reference.
string
Path to bowtie2 index
string
Path to GTF annotation file
string
Path to gene BED file
string
Path to genome blacklist
string
Name 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
string
K12-MG1655
Path to spike-in bowtie2 index
string
Path to spike-in fasta
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Do not load the iGenomes reference config.
boolean
Run pipeline up to input checking
boolean
Run pipeline up to reference preparation
boolean
Run pipeline up to pre-alignment
boolean
Run pipeline up to alignment
boolean
Run pipeline up to q-filtering
boolean
Run pipeline up to peak calling
boolean
Skips fastqc reporting
boolean
Skips trimming
boolean
Skips de-duplication
boolean
Skips reporting
boolean
Skips preseq reporting
boolean
Skips igv session generation
boolean
Skips deeptools QC repoting
boolean
Skips deeptools heatmap generation
boolean
Skips peak QC reporting
boolean
Skips multiqc
boolean
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integer
Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integer
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integer
Select aligner
string
bowtie2
Normalisation constant for spike-in read normalisation
integer
10000
Filter reads below a q-score threshold
integer
20
Filter mitochondrial reads
boolean
Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome.
string
De-duplicate target reads AND control reads (default is control only)
boolean
De-duplicate reads based on read 1 5’ start position. Relevant for assays using linear amplification with tagmentation (default is false).
boolean
Use —end-to-end mode of Bowtie2 during alignment
boolean
true
Sets the target read normalisation mode. Options are: [“Spikein”, “RPKM”, “CPM”, “BPM”, “None” ]
string
If normsalisation option is one of “RPKM”, “CPM”, “BPM” - then the binsize that the reads count is calculated on is used.
integer
50
Selects 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.
string
seacr
Specifies whether to use a control to normalise peak calls against (e.g. IgG)
boolean
true
Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks
boolean
true
Specifies whether the background control is scaled prior to being used to normalise peaks.
number
0.5
SEACR 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
number
0.05
SEACR normalization.
string
SEACR stringency.
string
Q-value threshold for MACS2 peak caller.
number
0.01
P-value threshold for macs2 peak caller. If set it will overide the qvalue.
number
parameter 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.
number
2700000000
Determines whether MACS2 broad or narrow peak mode is used for the peak caller
boolean
true
MACS2 broad cutoff parameter
number
0.1
Specifies what samples to group together for consensus peaks. Options are [group, all]
string
Minimum number of overlapping replicates needed for a consensus peak
number
1
Show gene names instead of symbols in IGV browser sessions
boolean
true
Deeptools multiBamSummary bam bin size
integer
500
Deeptools Correlation Plot statistical calculation method
string
pearson
Deeptools heatmap gene plot before length (bases)
integer
3000
Deeptools heatmap gene plot body length (bases)
integer
5000
Deeptools heatmap gene plot after length (bases)
integer
3000
Deeptools heatmap peak plot before length (bases)
integer
3000
Deeptools heatmap peak plot after length (bases)
integer
3000
Flag for whether to generate a heatmap for all samples together
boolean
true
Minimum fragment overlap for FriP score
number
0.2
Minimum peak overlap for peak reproducibility plot
number
0.2
Sort the IGV output tracks by group
boolean
true
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Pull Docker container.
boolean
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean