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$

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

required
type: string
default: ./results

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

type: string

Save genome reference data to the output directory

type: boolean

Save any technical replicate FASTQ files that were merged to the output directory

type: boolean

Save trimmed FASTQ files to the output directory

type: boolean

Save BAM files aligned to the spike-in genome to the output directory

type: boolean

Save unaligned sequences to the output directory

type: boolean

Save alignment intermediates to the output directory (WARNING: can be very large)

type: boolean

Email address for completion summary.

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

Output calculated scale factors from pipeline

type: boolean

Reference genome related files and options.

Name of iGenomes reference.

type: string

Path to bowtie2 index

type: string

Path to GTF annotation file

type: string

Path to gene BED file

type: string

Path to genome blacklist

type: string

Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6

type: string
default: K12-MG1655

Path to spike-in bowtie2 index

type: string

Path to spike-in fasta

type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Do not load the iGenomes reference config.

hidden
type: boolean

Run pipeline up to input checking

type: boolean

Run pipeline up to reference preparation

type: boolean

Run pipeline up to pre-alignment

type: boolean

Run pipeline up to alignment

type: boolean

Run pipeline up to q-filtering

type: boolean

Run pipeline up to peak calling

type: boolean

Skips fastqc reporting

type: boolean

Skips trimming

type: boolean

Skips de-duplication

type: boolean

Skips reporting

type: boolean

Skips preseq reporting

type: boolean

Skips igv session generation

type: boolean

Skips deeptools QC repoting

type: boolean

Skips deeptools heatmap generation

type: boolean

Skips peak QC reporting

type: boolean

Skips multiqc

type: boolean

Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).

type: integer

Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.

type: integer

Select aligner

hidden
type: string
default: bowtie2

Normalisation constant for spike-in read normalisation

hidden
type: integer
default: 10000

Filter reads below a q-score threshold

type: integer
default: 20

Filter mitochondrial reads

type: boolean

Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome.

type: string

De-duplicate target reads AND control reads (default is control only)

type: boolean

De-duplicate reads based on read 1 5’ start position. Relevant for assays using linear amplification with tagmentation (default is false).

type: boolean

Use —end-to-end mode of Bowtie2 during alignment

type: boolean
default: true

Sets the target read normalisation mode. Options are: [“Spikein”, “RPKM”, “CPM”, “BPM”, “None” ]

type: string

If normsalisation option is one of “RPKM”, “CPM”, “BPM” - then the binsize that the reads count is calculated on is used.

type: integer
default: 50

Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary peak callers will be run and outputed to the results folder.

type: string
default: seacr

Specifies whether to use a control to normalise peak calls against (e.g. IgG)

type: boolean
default: true

Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks

type: boolean
default: true

Specifies whether the background control is scaled prior to being used to normalise peaks.

type: number
default: 0.5

SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if --use_control is false

type: number
default: 0.05

SEACR normalization.

type: string

SEACR stringency.

type: string

Q-value threshold for MACS2 peak caller.

type: number
default: 0.01

P-value threshold for macs2 peak caller. If set it will overide the qvalue.

type: number

parameter required by MACS2. If using an iGenomes reference these have been provided when --genome is set as GRCh37, GRCh38, GRCm38, WBcel235, BDGP6, R64-1-1, EF2, hg38, hg19 and mm10. Otherwise the gsize will default to GRCh38.

type: number
default: 2700000000

Determines whether MACS2 broad or narrow peak mode is used for the peak caller

type: boolean
default: true

MACS2 broad cutoff parameter

type: number
default: 0.1

Specifies what samples to group together for consensus peaks. Options are [group, all]

type: string

Minimum number of overlapping replicates needed for a consensus peak

type: number
default: 1

Show gene names instead of symbols in IGV browser sessions

type: boolean
default: true

Deeptools multiBamSummary bam bin size

type: integer
default: 500

Deeptools Correlation Plot statistical calculation method

type: string
default: pearson

Deeptools heatmap gene plot before length (bases)

type: integer
default: 3000

Deeptools heatmap gene plot body length (bases)

type: integer
default: 5000

Deeptools heatmap gene plot after length (bases)

type: integer
default: 3000

Deeptools heatmap peak plot before length (bases)

type: integer
default: 3000

Deeptools heatmap peak plot after length (bases)

type: integer
default: 3000

Flag for whether to generate a heatmap for all samples together

type: boolean
default: true

Minimum fragment overlap for FriP score

type: number
default: 0.2

Minimum peak overlap for peak reproducibility plot

type: number
default: 0.2

Sort the IGV output tracks by group

type: boolean
default: true

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|d|day)\s*)+$

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

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Pull Docker container.

type: boolean

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

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean