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

Input FastQ or BAM files.

required
type: string

Input multiple FastQ or BAM files.

hidden
type: string
default: undefined

Specifies that the input is single-end reads.

type: boolean

Specifies that the input is in BAM format.

type: boolean

Specifies whether the input is DNA or RNA.

type: string
default: dna

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})$

Options for the optimisation step of the HLA typing pipeline.

Specifies the integer programming solver.

type: string
default: glpk

Specifies the number of output solutions.

type: integer
default: 1

Specifies the weight of the regularisation term.

type: number
default: 0.009

Options for the reference genome indices used to align reads.

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Do not load the iGenomes reference config.

hidden
type: boolean

Path for the mapping reference index location.

type: string
default: $baseDir/data/indices/yara

Name of the mapping reference index.

type: string

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

Email address for completion summary, only when pipeline fails.

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

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

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