nf-core/methylong
Extract methylation calls from long reads (ONT/ PacBio)
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.
stringThe 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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
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/Aligner option in ONT workflow, default is dorado aligner, specify minimap2 to switch
stringAligner option in PacBio workflow, default is pbmm2, specify minimap2 to switch
stringPileup method in PacBio workflow, default is pbcpgtools, specify modkit to switch
stringIndicate if required bedgraphs as output
booleanSpecify pbcpgtools pileup mode, default is using model mode, specify to switch to count mode
stringThis option will identify and output all CG sites found in the consensus sequence from the reads in the pb-CpG-toolspileup (reference free); by default reference sequences are used to identify and output all CG sites.
booleanSkip trimming in ONT workflow, will directly start from alignment step
booleanRemoves the alignment information added by aligners and updates flags accordingly
booleanIndicate if to skip snvcall and phase
booleanIndicate if required modcalling in PacBio workflow
booleanModcaller option in PacBio workflow, default is jasmine, specify ccsmeth to switch
stringDMRer option in DMR analysis for haplotype level, default is dss, specify modkit to switch
stringIndicate if required DMR analysis for population scale
booleanDMRer option in DMR analysis for population scale, default is dss, specify modkit to switch
stringOne of the group of DMR analysis in population scale
stringAnother group of DMR analysis in population scale
stringIndicate if required m6a calling
booleanCcsmeth call mods model.
stringSpecify dorado model, default is hac, other available models can be found on Dorado’s GitHub repository.
stringhacSpecify dorado modification, default is 5mCG_5hmCG, other available modifications can be found on Dorado’s GitHub repository.
string5mCG_5hmCGCustom 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.
stringFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string