Pipeline: sanger-tol/ensemblgenedownload (2.0.0)

Launch ID: 1721358890_838dbb9617aa

Go through the pipeline inputs below, setting them to the values that you would like. When you're done, click Launch and your parameters will be saved.

The page shown will show a command that you can use to directly launch the workflow. For those running on a system with no internet connection, you can copy the parameters JSON to a file and use the supplied command to launch.

Nextflow command-line flags
Nextflow command-line flags

General Nextflow flags to control how the pipeline runs.

These are not specific to the pipeline and will not be saved in any parameter file. They are just used when building the `nextflow run` launch command.
Must match pattern ^[a-zA-Z0-9-_]+$

Unique name for this nextflow run

Configuration profile

Work directory for intermediate files

Resume previous run, if found

Execute the script using the cached results, useful to continue executions that was stopped by an error

Input/output options

Define where the pipeline should find input data and save output data.

Must match pattern ^GCA_[0-9]{9}\.[0-9]+$

Accession number of the assembly to download. Typically of the form GCA_*.*

Must match pattern ^\S+$

Name of the species, as used by Ensembl. Note: it may differ from Tree of Life's

Must match pattern ^\S+$

Method used to annotate the genome. Typically ensembl, braker, etc.

Must match pattern ^20[0-9]{2}_[01][0-9]$

Version of the geneset, usually in the form YYYY_MM.

This parameter is required

The output directory where the results will be saved. Not considered for sample-sheet entries that have an absolute path.

Must match pattern ^\S+\.csv$

Path to comma-separated file containing information about the genesets to download. Used for bulk download of many genesets.

The file has to be a comma-separated file with five columns, and a header row. The columns names must be outdir, assembly_accession, ensembl_species_name, annotation_method, and geneset_version.