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.
string
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
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
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
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/
Aligner option in ONT workflow, default is dorado aligner, specify minimap2 to switch
string
Aligner option in PacBio workflow, default is pbmm2, specify minimap2 to switch
string
Pileup method in PacBio workflow, default is pbcpgtools, specify modkit to switch
string
Indicate if required bedgraphs as output
boolean
Specify pbcpgtools pileup mode, default is using model mode, specify to switch to count mode
string
This option will identify and output all CG sites found in the consensus sequence from the reads in the pb-CpG-tools
pileup (reference free); by default reference sequences are used to identify and output all CG sites.
boolean
Skip trimming in ONT workflow, will directly start from alignment step
boolean
Removes the alignment information added by aligners and updates flags accordingly
boolean
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
File size limit when attaching MultiQC reports to summary emails.
string
25.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