Pipeline: sanger-tol/variantcalling (1.1.4)

Launch ID: 1734831735_b458ef9f4276

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 ^\S+\.csv$

Path to comma-separated file containing information about the samples in the experiment.

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.

This parameter is required

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Path to directory or tar.gz archive for pre-built PacBio vector database.
Must match pattern ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

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.

Reference genome options

Reference genome related files and options required for the workflow.

This parameter is required

Path to FASTA genome file, either fasta or fast.gz.

Path to the index file of the FASTA genome file, either fai or gzi.

Align the input reads to the reference

Interval bed file.

Path to a file with a set of sites on the basis of a list of positions to include, Each line of the input file should contain a (tab-separated) chromosome and position.

Path to a file with a set of sites on the basis of a list of positions to exclude,Each line of the input file should contain a (tab-separated) chromosome and position.