nf-core/multiplesequencealign
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
Define where the pipeline should find input data and save output data.
Path to the samplesheet file containing information about datasets to be aligned and evaluated (samplesheet).
string^\S+\.(csv|tsv|yaml|yml|json)$You will need to create a file with information about the datasets before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with maximum 5 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringPath to the input fasta file.
string\S+\.f(n|ast)?a$Path to the input fasta file, it can be used in alternative to using the input samplesheet if you only have one dataset.
Path to a folder containing all the optional data files to be used (e.g. structures).
stringThis is a folder with all the optional data files to be used in the pipeline. It can be used in alternative to the samplesheet if you only have one dataset.
Suffix of the files given in the optional_data directory.
string.pdbTo provide additional data (e.g. protein structures), you must provide the path of a directory where thay are stored. Here, you can provide the suffix of the files in the given directory (e.g. pdb for pdb files).
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDefine which tools the pipeline should deploy.
Path to the file containing information about the tools to be deployed (toolsheet).
string^\S+\.(csv|tsv|yaml|yml|json)$You will need to create a file with information about the tools to be used before running the pipeline. Use this parameter to specify its location. It has to be a file with 4 columns, and a header row. See usage docs.
Tool to use for tree building.
stringThe tool to be used for tree building. If not set, the tree will not be built. This parameter is meant to be used in alternative to the toolsheet, in case you want to deploy only one tool.
Extra arguments for the tree building tool.
stringExtra arguments to be passed to the tree building tool. This parameter is meant to be used in alternative to the toolsheet, in case you want to deploy only one tool.
The aligner to be used.
stringThe aligner to be used. This parameter is meant to be used in alternative to the toolsheet, in case you want to deploy only one tool.
Extra arguments for the aligner tool.
stringExtra arguments to be passed to the aligner tool. This parameter is meant to be used in alternative to the toolsheet, in case you want to deploy only one tool.
Define 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 preprocessing step and use the files directly. Currently the preprocessing only features the structures where the header is cleaned.
Skip the validation of the input files.
booleanSkip the validation of the input files. This is not recommended, as it can lead to errors in the pipeline.
Skip the conversion of pdb files to fasta.
booleanSkip the conversion of pdb files to fasta. PDBs are converted if they are the only input file (no fasta) and are wished to be used either to run sequence-based aligners or sequence-based stats of the input files.
Define 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/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.
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.
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
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