nf-core/methylarray
Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
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 storage on Cloud infrastructure.
string
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
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
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
Less common options for the pipeline, typically set in a config file.
Display version and exit.
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
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
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string
Options related to the tools used in nf-core/methylarray.
Container link with the pipeline dependencies
string
docker.io/ajandriaa/methylarray:0.0.5dev
Path to comma-separated file containing extra information about the samples in the experiment
string
Version of bsgenome to use
string
hg38
Path to the bisulfite-converted reference genome generated with ‘DNAmCrosshyb’ utility scripts
string
Whether to compute DMRs
boolean
true
Run XREACTIVE_PROBES_FIND_REMOVE?
boolean
true
String passed to ‘chromosomes’ argument in ‘map_probes()’ function from ‘DNAmCrosshyb’ R package in ‘XREACTIVE_PROBES_FIND_REMOVE’ process
string
all
Run REMOVE_SNP_PROBES?
boolean
true
Whether to run optional processes
boolean
true
Whether to remove sex chromosomes in an optional step
boolean
true
Whether to remove confounding probes in an optional step
boolean
true
Whether to adjust the data for cell composition in an optional step
boolean
true
Whether to adjust the data for batch effects in an optional step
boolean
true
Whether to compute blocks of DNA regions with many DMPs
boolean