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$
Path to the output directory where the results will be saved.
string
./results
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Save reference data to output directory
boolean
Save any technical replicates that were merged to output directory
boolean
Save trimmed fastqs to output directory
boolean
Save bam files aligned to the spike-in genome to output directory
boolean
Save unaligned sequences to output directory
boolean
Save alignment intermediates to output directory (WARNING: can be very large)
boolean
Select aligner
string
bowtie2
Trim galore param
integer
Trim galore param
integer
Trim galore param
integer
Trim galore param
integer
Trim galore param
integer
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to bowtie2 index
string
Path to GTF annotation file
string
Path to genome blacklist
string
Name of the igenome reference for the spike-in genome
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)?$
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Filter reads below a q-score threshold
integer
Deduplicate non-control reads
boolean
Normalisation constant
integer
10000
Specifies if the samplesheet contains an IgG control
boolean
true
Threshold for peak calling when no IgG is present
number
0.05
Path to gene bed file
string
Minimum number of overlapping replicates needed for a consensus peak
integer
1
Run pipeline up to reference preparation
boolean
Run pipeline up to input checking
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 scalefactor normalisation
boolean
Skips reporting
boolean
Skips igv session generation
boolean
Skips deeptools heatmaps
boolean
Skips multiqc
boolean
Skip upset plot calculation
boolean
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|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
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
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean
Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
boolean