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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringPath to the input fasta file.
stringPath to a folder containing all the optional data files to be used (e.g. structures).
stringSuffix of the files given in the optional_data directory.
string.pdbEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDefine 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.
stringExtra arguments for the tree building tool.
stringThe aligner to be used.
stringExtra arguments for the aligner tool.
stringDefine wether and how to run compression
Run on CPUs (default) or GPUs
booleanProduce uncompressed alignment files
booleanSkip the preprocessing step for the input files.
booleanSkip the validation of the input files.
booleanSkip the conversion of pdb files to fasta.
booleanDefine 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.
booleanDefine wether to run stats.
Skip all of the evaluations computation on the msa.
booleanCalculate the Sum of Pairs of alignment.
booleantrueCalculate the Total Column Score of alignment.
booleantrueCalculate the iRMSD of alignment.
booleanCalculate the Transitive Consistency Score (TCS) of alignment.
booleanExtract total number of gaps and average number of gaps of the alignment.
booleantrueDefine wether to run stats.
Skip the multiqc report generation.
booleanSkip the shiny report generation.
booleanFolder containing the main shiny app.
stringSkip the visualization generation.
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.
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