Introduction Usage Parameters Output Results Releases

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

The input design file for the pipeline.

required
type: string

The output directory where the results will be saved.

type: string
default: ./results

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Workflow name.

hidden
type: string

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

Do not use coloured log outputs.

hidden
type: boolean

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info
type: string
default: s3://ngi-igenomes/igenomes/
type: string
default: true

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

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

hidden
type: integer
default: 16

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

hidden
type: string
default: 128.GB

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

hidden
type: string
default: 240.h

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional configs hostname.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Path to Kraken2 database.

type: string

Parameters for the assembly

The assembler to use for assembly. Available options are Unicycler, Canu, Miniasm. The latter two are only available for long-read data, whereas Unicycler can be used for short or hybrid assembly projects.

type: string
default: unicycler

Which type of assembly to perform.

type: string
default: short

Extra arguments for Unicycler

type: string

This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.

type: string

The annotation method to annotate the final assembly. Default choice is prokka, but the dfast tool is also available. For the latter, make sure to create your specific config if you’re not happy with the default one provided. See #dfast_config to find out how.

type: string
default: prokka

Extra arguments for prokka annotation tool.

type: string

Specifies a configuration file for the DFAST annotation method. This can be used instead of PROKKA if required to specify a specific config file for annotation. If you want to know how to create your config file, please refer to the DFAST readme on how to create one. > The default config is just included for testing, so if you want to annotate using DFAST, you have to create a config!

type: string
default: /Users/alexanderpeltzer/IDEA/nf-core/bacass/assets/test_config_dfast.py

Which assembly polishing method to use.

type: string
default: medaka

Skip running Kraken2 classifier on reads.

type: string

Skip annotating the assembly with Prokka /DFAST.

type: string

Skip running PycoQC on long read input.

type: string

Skip polishing the long-read assembly with FAST5 input. Will not affect short/hybrid assemblies.

type: string
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