nf-core/pairgenomealign
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
1.0.0
). The latest
stable release is
2.2.0
.
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$
Path or URL to a FASTA genome file for the target genome.
string
^\S+\.fn?a(sta)?(\.gz)?$
Target genome name.
string
target
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
Arguments for the lastdb, last-train, lastal and last-split programs.
Make a many to many alignment
boolean
Select the the LAST seed to index the target genome.
string
Path to a file containing alignment parameters or a scoring matrix. If this option is used, last-train
will be skipped and alignment parameters will be the same for each query.
string
Arguments passed to both last-train
and lastal
.
string
-C2 -D1e9
Arguments passed only to lastal
(useful when they are not recognised by last-train
).
string
Mismap probability cutoff for last-split
.
string
0.00001
Customise dot-plots or skip them.
Extra arguments passed to last-dotplot
to customise the output. See https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst.
string
Do not generate the one-to-many alignment dot-plot.
boolean
Do not generate the one-to-one alignment dot-plot.
boolean
Do not generate the many-to-one alignment dot-plot.
boolean
Do not generate the many-to-many alignment dot-plot.
boolean
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
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
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
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
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/