Launch pipeline » sanger-tol

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.

-name

Must match pattern ^[a-zA-Z0-9-_]+$

Unique name for this nextflow run

-profile

Configuration profile

-work-dir

Work directory for intermediate files

-resume

True

False

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.

--input^*

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. See usage docs.

--binsize^*

Must be an integer

Bin size in base pairs for cooler cload

--kmer_size^*

Must be an integer

Size for Fastk to create the k-mer library

--assembly^*

This parameter is required

The Genbank assembly accession for the assembly, for example: GCA_922984935.2.

--biosample_wgs^*

This parameter is required

The biosample accesion(s) linked to the WGS samples in the experiment, for example: SAMEA7520803.

--biosample_rna

The biosample accesion(s) linked to the RNA samples in the experiment, for example: SAMEA7521081.

--biosample_hic

The biosample accesion(s) linked to the Hi-C samples in the experiment, for example: SAMEA7520846.

--outdir^*

This parameter is required

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

--email

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.

--multiqc_title

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

--cool_order

Path to a file that contains the sequence names in the order you want to represent them on the contact-map.

If not specified, the pipeline will use the sequences in the same order they are listed by the NCI, which follows the karyotype.

--write_to_portal

True

False

Flag to control if results are written to genome notes portal database .

--genome_notes_api

URL for Genome Notes Portal API .

--note_template

The path to a genome note template file.

Set this parameter if you have a genome note template file that you wish to populate. Templates may be docx or xml files

--upload_higlass_data

True

False

flag to control if Higlass server should be updated to add new files

--higlass_url

URL for the Higlass server

--higlass_upload_directory

The ingress directory for the kubernetes cluster running the HiGlass server.

--higlass_data_project_dir

Subdirectory struture to use for organising HiGlass data, suggested format is / e.g. '/asg/algae'

--higlass_kubeconfig

The path to the kubeconfig for the kubernetes cluster running the HiGlass server.

--higlass_deployment_name

Name of the kubernetes deployment for the HiGlass server.

--higlass_namespace

The name for the namespace used in the Kubernetes cluster running the HiGlass server.

Databases

Define where the pipeline should find databases.

--lineage_db

Local directory where clade-specific BUSCO lineage datasets are stored.

--lineage_tax_ids

Local file that holds a mapping between BUSCO lineages and taxon IDs.

Initialised from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz

Reference genome options

Reference genome related files and options required for the workflow.

--fasta^*

Must match pattern ^\S+\.fn?a(sta)?(\.gz)?$

Path to FASTA genome file.

Execution

Control the execution of the pipeline.

--use_work_dir_as_temp

True

False

Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.

Institutional config options

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.

--custom_config_version

Git commit id for Institutional configs.

--custom_config_base

Base directory for Institutional configs.

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.

--config_profile_name

Institutional config name.

--config_profile_description

Institutional config description.

--config_profile_contact

Institutional config contact information.

--config_profile_url

Institutional config URL link.

Max job request options

Set the top limit for requested resources for any single job.

If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system. Note that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.

--max_cpus

Must be an integer

Maximum number of CPUs that can be requested for any single job.

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

--max_memory

Must match pattern ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of memory that can be requested for any single job.

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

--max_time

Must match pattern ^(\d+\.?\s*(s|m|h|day)\s*)+$

Maximum amount of time that can be requested for any single job.

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'