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
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.
stringtargetSkip assembly QC.
booleanfalseThe 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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSelect the LAST seed to index the target genome.
stringCustomise the way to mask the target genome.
stringArguments for the lastdb, last-train, lastal and last-split programs.
Convert the final one-to-one alignment to a different format than MAF.
stringno_exportMake a many to many alignment
booleanPath to a file containing alignment parameters or a scoring matrix. If this option is used, last-train will be skipped and alignment parameters will be the same for each query.
stringArguments passed to both last-train and lastal.
string-C2 -D1e9Arguments passed only to lastal (useful when they are not recognised by last-train).
stringMismap probability cutoff for last-split.
string0.00001Customise dot-plots or skip them.
Maximum width of the dot plots, in pixels.
integer1000Maximum height of the dot plots, in pixels.
integer10000Font size of the sequence names on the dot plots.
integer14Extra arguments passed to last-dotplot to customise the output. See https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst.
stringDo not generate the one-to-many alignment dot-plot.
booleanDo not generate the one-to-one alignment dot-plot.
booleanDo not generate the many-to-one alignment dot-plot.
booleanDo not generate the many-to-many alignment dot-plot.
booleanRemove isolated alignments with the maf-filter tool.
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$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.
string