nf-core/multiplesequencealign
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
1.1.0
). The latest
stable release is
1.1.1
.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about datasets to be aligned and evaluated (samplesheet).
string
^\S+\.csv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Path to the input fasta file.
string
Path to a folder containing all the optional data files to be used (e.g. structures).
string
Suffix of the files given in the optional_data directory.
string
.pdb
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
Define which tools the pipeline should deploy.
Path to comma-separated file containing information about the tools to be deloyed (toolsheet).
string
^\S+\.csv$
Tool to use for tree building.
string
Extra arguments for the tree building tool.
string
The aligner to be used.
string
Extra arguments for the aligner tool.
string
Define wether and how to run compression
Run on CPUs (default) or GPUs
boolean
Produce uncompressed alignment files
boolean
Skip the preprocessing step for the input files.
boolean
Skip the validation of the input files.
boolean
Skip the conversion of pdb files to fasta.
boolean
Define extra alignment options.
Build consensus alignment with M-COFFEE.
boolean
Define wether to run stats.
Skip all of the statistics computation on the fasta file.
boolean
Calculate the percentage similarity across the sequences in the input files.
boolean
Calculate general statistics on input files.
boolean
Extract plddt from structure files. Only works if the files have been generated by AF2.
boolean
Define wether to run stats.
Skip all of the evaluations computation on the msa.
boolean
Calculate the Sum of Pairs of alignment.
boolean
true
Calculate the Total Column Score of alignment.
boolean
true
Calculate the iRMSD of alignment.
boolean
Calculate the Transitive Consistency Score (TCS) of alignment.
boolean
Extract total number of gaps and average number of gaps of the alignment.
boolean
true
Define wether to run stats.
Skip the multiqc report generation.
boolean
Skip the shiny report generation.
boolean
Folder containing the main shiny app.
string
Skip the visualization generation.
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
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
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
Base URL or local path to location of pipeline test dataset files
string
https://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