Pipeline: sanger-tol/curationpretext (1.0.1)

Launch ID: 1732350048_a08b4df6c3bc

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+\.fn?a(sta)?(\.gz)?$

Input fasta file

You need the input fasta file

Input longread fasta directory

You need the input fasta file directory

Type of longread data

Choose between {'hifi', 'illumina', 'ont'}

This parameter is required

Input cram directory

You need the input fasta file directory

Telomeric Motif for search. Defaults to TTAGGG

Give me a telomeric motif

This parameter is required

HiC map scaffold order. Default to unsorted

How you want to display your hic map, sorted by length?

Aligner for use {minimap2, bwamem2} in generating map

Pick between {minimap2, bwamem2}. Defaults to 'minimap2'

This parameter is required

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

This parameter is required

A Name for the sample