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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Path or URL to a FASTA genome file for the target genome.
string^\S+\.fn?a(sta)?(\.gz)?$Target genome name.
stringtargetBy default the target genome is named target and this name is concatenated with the sample IDs using ___ as a separator to construct alignment file names. Use this option to provide a more informative name for the target genome.
The 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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSelect the the LAST seed to index the target genome.
stringLAST creates a database of seed sequences in the target genome, and provides different ways to generate these seeds. The default (YASS) searches for long-and-weak similarities that allow for mismatches but not gaps. Among alternatives, there are NEAR for short-and-strong (near-identical) similarities with many gaps (insertions and deletions), MAM8 to find weak similarities with high sensitivity, but low speed and high memory usage, or RY128 that reduces run time and memory use, by only seeking seeds at ~1/128 of positions in each sequence, which is useful when the purpose of running this pipeline is only to generate whole-genome dotplots, or when sensitivity for tiny fragments may be unnecessary or undesirable. See https://gitlab.com/mcfrith/last/-/blob/main/doc/last-seeds.rst for details.
Customise the way to mask the target genome.
stringIn this pipeline, letters soft-masked in lowercase are excluded from indexing (lastdb -c). By default, the original mask is removed and a new one is made with an internal verison of the “tantan” tool. Set this option to original to keep the orininal soft-masking. See https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst for details.
Arguments for the lastdb, last-train, lastal and last-split programs.
Make a many to many alignment
booleanThis adds time and can comsume considerable amount of space; use only if you need that data, for instance in the case of a self-alignment
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.
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.
Extra 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.
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/