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

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

required
type: string
pattern: ^\S+\.(csv|tsv|txt)$

A CSV file describing sample contrasts

required
type: string
pattern: ^\S+\.csv$

TSV-format abundance matrix

required
type: string
pattern: ^\S+\.(tsv|csv|txt)$

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

required
type: string

A string to identify results in the output directory

required
type: string
default: study

A string identifying the technology used to produce the data

required
type: string

Email address for completion summary.

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

A text file listing technical features (e.g. spikes)

type: string

When set, use the control features in scaling/ normalisation

type: boolean

Rmd report template from which to create the pipeline report

required
type: string
pattern: ^\S+\.Rmd$

A logo to display in the report instead of the generic pipeline logo

required
type: string
default: docs/images/nf-core-differentialabundance_logo_light.png

CSS to use to style the output, in lieu of the default nf-core styling

required
type: string
default: assets/nf-core_style.css

A markdown file containing citations to include in the fiinal report

type: string
default: CITATIONS.md

Column in the samples sheet to be used as the primary sample identifier

required
type: string
default: sample

Type of observation

required
type: string
default: sample

Options related to features

Feature ID attribute in the GTF file (e.g. the gene_id field)

required
type: string
default: gene_id

Feature name attribute in the GTF file (e.g. the gene symbol field)

required
type: string
default: gene_name

Type of feature we have, often ‘gene’

required
type: string
default: gene

Options related to filtering upstream of differential analysis

Minimum abundance value

required
type: integer
default: 1

Minimum observations that must pass the threshold to retain the row/ feature (e.g. gene).

type: number
default: 1

A minimum proportion of observations, given as a number between 0 and 1, that must pass the threshold. Overrides minimum_samples

type: number

An optional grouping variable to be used to calculate a min_samples value

type: string

Options related to data exploration

Clustering method used in dendrogram creation

required
type: string
default: ward.D2

Correlation method used in dendrogram creation

required
type: string
default: spearman

Number of features selected before certain exploratory analyses

required
type: integer
default: 500

Length of the whiskers in boxplots as multiple of IQR. Defaults to 1.5.

type: number
default: 1.5

Threshold on MAD score for outlier identification

type: integer
default: -5

How should the main grouping variable be selected? ‘auto_pca’, ‘contrasts’, or a valid column name from the observations table.

required
type: string
default: auto_pca

Options related to differential operations

The suffix associated tabular differential results tables

required
type: string
default: .deseq2.results.tsv

The feature identifier column in differential results tables

required
type: string
default: gene_id

The fold change column in differential results tables

required
type: string
default: log2FoldChange

The p value column in differential results tables

type: string
default: pvalue

The q value column in differential results tables.

required
type: string
default: padj

Minimum fold change used to calculate differential feature numbers

required
type: integer
default: 2

Maximum q value used to calculate differential feature numbrers

required
type: number
default: 0.05

Where a features file (GTF) has been provided, what attributed to use to name features

type: string
default: gene_name

Indicate whether or not fold changes are on the log scale (default is to assume they are)

type: boolean
default: true

test parameter passed to DESeq()

type: string

fitType parameter passed to DESeq()

type: string

sfType parameter passed to DESeq()

type: string

‘minReplicatesForReplace’ parameter passed to DESeq()

type: integer
default: 7

useT parameter passed to DESeq2

type: boolean

independentFiltering parameter passed to results()

type: boolean
default: true

lfcThreshold parameter passed to results()

type: integer

altHypothesis parameter passed to results()

type: string
default: greaterAbs

pAdjustMethod parameter passed to results()

type: string
default: BH

alpha parameter passed to results()

type: number
default: 0.1

minmu parameter passed to results()

type: number
default: 0.5

variance stabilisation method to use when making a variance stabilised matrix

type: string

Shink fold changes in results?

type: boolean
default: true

Number of cores

type: integer
default: 1

blind parameter for rlog() and/ or vst()

type: boolean
default: true

nsub parameter passed to vst()

type: integer
default: 1000

Set to run GSEA to infer differential gene sets in contrasts

type: boolean

Permutation type

type: string

Number of permutations

type: integer
default: 1000

Enrichment statistic

type: string

Metric for ranking genes

type: string

Gene list sorting mode

type: string

Gene list ordering mode

type: string

Max size: exclude larger sets

type: integer
default: 500

Min size: exclude smaller sets

type: integer
default: 15

Normalisation mode

type: string

Randomization mode

type: string

Make detailed geneset report?

type: boolean
default: true

Use median for class metrics

type: boolean

Number of markers

type: integer
default: 100

Plot graphs for the top sets of each phenotype

type: integer
default: 20

Seed for permutation

type: string
default: timestamp

Save random ranked lists

type: boolean

Make a zipped file with all reports

type: boolean

Gene sets in GMT or GMX-format

type: string
default: None

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Genome annotation file in GTF format

type: string
pattern: ^\S+\.gtf(\.gz)?

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

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 config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

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

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

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

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

Display help text.

type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

type: string

Email address for completion summary, only when pipeline fails.

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

Send plain-text email instead of HTML.

type: boolean

Do not use coloured log outputs.

type: boolean

Incoming hook URL for messaging service

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

type: boolean
default: true

Show all params when using --help

type: boolean