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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://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.
stringOptions related to the tools used in nf-core/methylarray.
Container link with the pipeline dependencies
stringdocker.io/ajandriaa/methylarray:0.0.5devPath to comma-separated file containing extra information about the samples in the experiment
stringVersion of bsgenome to use
stringhg38Path to the bisulfite-converted reference genome generated with ‘DNAmCrosshyb’ utility scripts
stringWhether to compute DMRs
booleantrueRun XREACTIVE_PROBES_FIND_REMOVE?
booleantrueString passed to ‘chromosomes’ argument in ‘map_probes()’ function from ‘DNAmCrosshyb’ R package in ‘XREACTIVE_PROBES_FIND_REMOVE’ process
stringallRun REMOVE_SNP_PROBES?
booleantrueWhether to run optional processes
booleantrueWhether to remove sex chromosomes in an optional step
booleantrueWhether to remove confounding probes in an optional step
booleantrueWhether to adjust the data for cell composition in an optional step
booleantrueWhether to adjust the data for batch effects in an optional step
booleantrueWhether to compute blocks of DNA regions with many DMPs
boolean