Parameters
Accession number of the assembly to download. Typically of the form GCA_*.*
The output directory where the results will be saved. Not considered for sample-sheet entries that have an absolute path.
default: 'results'Path to comma-separated file containing information about the assemblies to download. Used for bulk download of many assemblies.
You will need to create a file with information about the assemblies you want to download. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
pattern: ^\S+\.csv$Root location of the NCBI FTP, in which all assemblies can be found. Access protocol is actually not limited to FTP, and we use HTTPS by default.
default: 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA'Email address for completion summary.
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters 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/'Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.