nf-core/multiplesequencealign
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
1.0.0). 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 the samples in the experiment.
string^\S+\.csv$Path to comma-separated file containing information about the tools to be used in the experiment.
string^\S+\.csv$Suffix of the dependencies templates.
stringThe 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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDefine extra alignment options.
Build consensus alignment with M-COFFEE.
booleanDefine wether to run stats.
Skip all of the statistics computation on the fasta file.
booleanCalculate the percentage similarity across the sequences in the input files.
booleanCalculate general statistics on input files.
booleanExtract plddt from structure files. Only works if the files have been generated by AF2.
booleanExtract total number of gaps and average number of gaps of the alignment.
booleanDefine wether to run stats.
Skip all of the evaluations computation on the msa.
booleanCalculate the Sum of Pairs of alignment.
booleanCalculate the Total Column Score of alignment.
booleanCalculate the iRMSD of alignment.
booleanCalculate the Transitive Consistency Score (TCS) of alignment.
booleanDefine wether to run stats.
Skip the multiqc report generation.
booleanSkip the shiny report generation.
booleanFile containing the main shiny app.
stringvariable containing the shiny_trace mode to be used.
stringDefine wether and how to run compression
Produce uncompressed alignment files
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
booleanBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/