Parameters
Path to YAML file describing the input data.
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.
pattern: ^\S+\.(yaml|yml)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Email address for completion summary.
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
pattern: ^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$Predict ribosomal RNA (rRNA) genes in assemblies using Infernal and the included Rfam covariance models.
default: 1Covariance model for rRNA preditiction from RFAM.
default: '${projectDir}/assets/rRNA.cm'Enable Genomad for classification of circular contigs for determination of plasmid status.
default: 1Path to a directory containing a Genomad database. If not provided, the database will be downloaded automatically.
The number of chunks to split the Genomad database into when running searches. Increasing this value decreases memory usage at the expense of runtime.
default: 1When mapping Hi-C, map each CRAM file in slices of this size.
default: 10000Minimum map quality for a Hi-C read to be passed on for binning by Bin3C or Metator.
default: 60Which method to use to merge the chunked Hi-C bam files back together. One of "merge" (samtools merge) or "cat" (samtools cat).
"merge" is safer and uses samtools merge, which will ensure that the name sorting is retained among all reads in the final output bam. However, in cases where there is a lot of Hi-C data, the merge operation can be very slow. In this case, "cat" is presented as an alternative, using heuristics to concatenate the bam files together using samtools cat. This requires that the initial input CRAM files are sorted by read name so that the chunks represent sets of consecutively named reads, and may fall down when there are multiple Hi-C CRAM libraries, especially if there are multiple read groups in a single library.
The minimum size of contig to be considered when binning. This option applies to MetaBat2, MaxBin2, and Bin3C, but not Metator.
default: 3000The minimum required percent identity of a read mapping to the assembly to be counted during coverage estimation for MetaBat2 and MaxBin2.
default: 97The minimum size of a bin, in basepairs, to be emitted. This parameter is currently respected by MetaBat2 and Bin3C, but not Metator or MaxBin2.
default: 150000Path to the GTDB r207 Pfam HMM database.
default: '${projectDir}/assets/gtdbtk_rel207_Pfam-A.hmm'Path to the GTDB r207 TigrFam HMM database.
default: '${projectDir}/assets/gtdbtk_rel207_tigrfam.hmm'Path to a local diamond database file for CheckM2. If not provided, the CheckM2 database will automatically be downloaded.
Path to the GTDB-Tk bac120 metadata file.
default: 'https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/bac120_metadata_r220.tsv.gz'Path to the GTDB-Tk ar53 metadata file.
default: 'https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/ar53_metadata_r220.tsv.gz'Minimum CheckM2 completeness required for a bin to be classified by GTDB-Tk.
default: 50Maximum contamination allowed CheckM2 completeness for a bin to be classified by GTDB-Tk.
default: 10Path to directory containing the names.dmp, nodes.dmp, delnodes.dmp, and merged.dmp files from the NCBI taxdump archive (ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz)
Multiplier for completeness when scoring bins for the bin summary. Used in formula (compleneness_score completeness - contamination_score contamination).
default: 1Multiplier for contamination when scoring bins for the bin summary. Used in formula (compleneness_score completeness - contamination_score contamination).
default: 0.5Parameters used to describe centralised config profiles. These should not be edited.
The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.
Git commit id for Institutional configs.
default: 'master'Base directory for Institutional configs.
default: 'https://raw.githubusercontent.com/nf-core/configs/master'If 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.
Less common options for the pipeline, typically set in a config file.
These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.
Typically these options would be set in a Nextflow config file loaded for all pipeline runs, such as ~/.nextflow/config.
Method used to save pipeline results to output directory.
The 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.
An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Incoming hook URL for messaging service
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
default: 1Base URL or local path to location of pipeline test dataset files
default: 'https://raw.githubusercontent.com/nf-core/test-datasets/'Base URL or local path to location of pipeline test dataset files
default: 'https://tolit.cog.sanger.ac.uk/test-data/'