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 containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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.
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.
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
number0.5mmseqs parameter for minimum sequence coverage ratio
number0.9mmseqs parameter for coverage mode: 0 for both, 1 for target and 2 for query sequence
integerSave 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.
integer25Use 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 seed MSA gaps
booleantrueChoose clipping tool. ClipKIT clips gaps throughout the sequence while clip_ends only at the ends.
stringAvailable tools: local module 'clip_ends' or nf-core 'clipkit'.
Seed MSA positions with gappyness greater than this threshold will be trimmed
number0.5Set to true to recruit additional sequences from the input FASTA file using the family HMMs to refine the alignments
booleantrueBoolean whether to generate target results file of hmmsearch
booleanBoolean whether to generate domain results file of hmmsearch
booleantruehmmsearch e-value cutoff threshold for reported results
number0.001Save the output of hmmsearch (stockholm msa and domtblout)
booleanSpecify to save the .sto.gz and .domtbl.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
number0.8Use these parameters to control the redundancy removal subworkflow execution.
Removal of between-family redundancy via hmmsearch.
booleantruehmmsearch minimum length percentage filter of hit env vs query length, for redundant family removal
number0.8Removal of inside-family redundancy of sequences via mmseqs clustering.
booleantruemmseqs parameter for minimum sequence identity
number0.95mmseqs parameter for minimum sequence coverage ratio
number0.95mmseqs parameter for coverage mode: 0 for both, 1 for target and 2 for query sequence
integer