nf-core/proteinfamilies
Generation and update of protein families
Define where the pipeline should find input data and save output data.
Path to comma-separated file '.csv' containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file '.csv' with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringYou will need to define where your results will be saved. Use this parameter to specify the location.
Email address for completion summary. Example: name.surname@example.com
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringParameters 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. Example: name.surname@example.com
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails. Example: name.surname@example.com
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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/proteinfamilies/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringUse these parameters to control the flow of the clustering subworkflow execution.
Save the db output folder of mmseqs createdb
booleanSpecify to save the mmseqs formatted database of input fasta sequences.
Choose clustering algorithm. Either simple 'cluster' for medium size inputs, or 'linclust' for less sensitive clustering of larger datasets.
stringmmseqs algorithms available: 'cluster' or 'linclust'.
mmseqs parameter for minimum sequence identity
number0.5Minimum sequence identity required for clustering. The mmseqs default is 0.9, but protein families contain way more diverse sequences (https://doi.org/10.1093/protein/12.2.85).
mmseqs parameter for minimum sequence coverage ratio
number0.9Minimum sequence length coverage required for clustering
mmseqs parameter for coverage mode: 0 for both, 1 for target and 2 for query sequence
integerDefined by the number of aligned residue pairs divided by 0: the maximum of the length of query/centre and target/non-centre sequences, 1: the length of the target/non-centre sequence, 2: the length of the query/centre
Save the clustering output folder of mmseqs cluster or linclust
booleanSpecify to save the mmseqs formatted result clustering.
Minimum clustering chunk size threshold to create seed Multiple Sequence Alignments upon.
integer25This is an initial filter for the mmseqs clustering results. The lower the threshold, the more families will be generated. Additional sequences may be later recruited in the families.
Save membership-filtered initial mmseqs clusters in fasta format
booleanSpecify to save the mmseqs clusters in fasta format.
Use these parameters to control the Multiple Sequence Alignment subworkflow execution.
Choose alignment tool. FAMSA is recommended as best time-memory-accuracy combination option.
stringAvailable tools: 'famsa' or 'mafft'.
Boolean whether to trim the Multiple Sequence Alignment (MSA) gaps
booleantrueChoose the output format of the clipped alignment.
stringclipkitMake sure this is different than the input extension format, otherwise the tool won't run (i.e., != aln for famsa and != fas for mafft).
Choose if ClipKIT should only clip gaps at the ends of the MSAs.
booleantrueBy default, ClipKIT clips gaps over the specified threshold, both at the ends and throughout the length of the MSA. This flag restricts clipping to the ends
Multiple Sequence Alignment (MSA) positions with gappiness greater than this threshold will be trimmed
number0.5Set to true to recruit additional sequences from the input FASTA file using the family Hidden Markov Models (HMMs) to refine the alignments
booleantrueIf this is set to true, the hmmer/hmmsearch module will be used to recruit additional sequences from the input fasta file into the family (above the hmmsearch_query_length_threshold), resulting in bigger but better described families
Boolean whether to generate target results file of hmmsearch
booleanSpecify to calculate the hmmsearch tabular (space-delimited) summary of per-target output (*.tbl.gz).
Boolean whether to generate domain results file of hmmsearch
booleantrueSpecify to calculate the hmmsearch tabular (space-delimited) summary of per-domain output (*.domtbl.gz).
hmmsearch e-value cutoff threshold for reported results
number0.001Save the output of hmmsearch (.domtbl.gz and .tbl.gz)
booleanSpecify to save the .domtbl.gz and .tbl.gz files generated by running hmmsearch on the family model against the input set of sequences.
hmmsearch minimum length percentage filter of hit env vs query length
number0.9This length threshold should be quite high to make sure that small, fragmented sequences are not recruited in the family models
Save family fasta files after recruiting sequences with hmmsearch
booleanSpecify to save the extended family fasta files with all hmmsearch recruited sequences.
Use these parameters to control the redundancy removal subworkflow execution.
Removal of between-family redundancy via hmmsearch.
booleantrueSimilar families should not be further processed, for better resource management and to avoid duplication of families.
hmmsearch minimum length percentage filter of hit env vs query length, for redundant family removal
number0.9Save only the fasta files of non-redundant families (might still contain redundant sequences)
booleanSpecify to save the fasta files of non-redundant families.
Removal of inside-family redundancy of sequences via mmseqs clustering.
booleantrueHighly similar sequences within the same family should be removed, while making sure that the protein family diversity is still well captured.
mmseqs parameter for minimum sequence identity
number0.9Need to be quite high, to make sure that the diversity is still well captured, while highly similar sequences are removed
mmseqs parameter for minimum sequence coverage ratio
number0.9Need to be quite high, to make sure that the diversity is still well captured, well highly similar sequences are removed
mmseqs parameter for coverage mode: 0 for both, 1 for target and 2 for query sequence
integerDefined by the number of aligned residue pairs divided by 0: the maximum of the length of query/centre and target/non-centre sequences, 1: the length of the target/non-centre sequence, 2: the length of the query/centre
Save the final family fasta files with sequence redundancy removed
booleanSpecify to save the family fasta files with non-redundant sequence sets.