nf-core/phyloplace
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about phylogenetic placements to perform.
string^\S+\.csv$This specifies parameters for direct phylogenetic placement of query sequences onto a reference phylogeny, in contrast to when a HMMER search is first performed, see --phylosearch_input. It has to be a comma-separated file with at least five columns, and a header row ('sample', 'queryseqfile', 'refseqfile', 'refphylogeny' and 'model'). See usage docs.
Path to comma-separated file containing information about phylogenetic searches to perform.
string^\S+\.csv$This specifies parameters for phylogenetic placement of unknown sequences onto reference phylogeny after first using HMMER to search through a collection of uknown sequences (see --search_fasta) in contrast to when only placing known query sequences, see --phyloplace_input. It has to be a comma-separated file with at least two columns that specifies search HMM profiles ('target' and 'hmm') and at least three columns specifying the reference phylogenies ('refseqfile', 'refphylogeny' and 'model') for placement of search results. (Decoy profiles, i.e. profiles only used for searches, not placements, are allowed.) See usage docs.
Fasta file with sequences to be searched with HMM profiles.
stringSequences from this file matching an HMM profile, will be placed in the reference phylogeny corresponding to the HMM profile.
Name of analysis
stringplacementMethod used to align query sequences with.
stringQuery sequences will be aligned to the reference alignment using either HMMER, Clustal Omega or MAFFT, except when an hmm profile is provided (--hmmfile; implies that --alignmethod is set to 'hmmer'), in which case both the reference and query sequences will be aligned with the profile (reference sequences must not be aligned, i.e. must not contain '-' characters).
Fasta file with query sequences
stringFile with reference sequences. Any format supported by HMMER tools.
stringIf the sequences are not aligned, you need to provide an alignment option, e.g. --hmmfile.
HMM file. If provided, will be used to align both the reference and query sequences.
stringNewick file with aligned reference sequences.
stringEvolutionary model to use for placement, e.g. 'LG'.
stringTab-separated file with taxonomy assignments of reference sequences.
string^\S+\.tsv$The first column should consist of names of reference sequences, the second of taxonomy strings, e.g. 'Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli'.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
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.
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
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/