nf-core/omicsgenetraitassociation
A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
Parameters to modify MEA behavior
Column name for gene ID/names
string
markname
Column name for p-values
string
meta_p
Number of tests for multiple testing
integer
17551
P-value threshold alpha value
number
0.05
Parameters to modify MMAP behavior
Whether MMAP output has a header or not
integer
1
Column name or number for p-values
string
p_vals
Column name or number for Beta values
string
betas_genes
Column name or number for SE values
string
se_genes
Parameters to modify PASCAL behavior
Whether PASCAL output has a header or not
integer
Column name or number for p-values
integer
1
Define where the pipeline should find input data and save output data.
path to samplesheet
string
output directory
string
results
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|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
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
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean