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$

Path to 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})$

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

type: string

Save reference data to output directory

type: boolean

Save any technical replicates that were merged to output directory

type: boolean

Save trimmed fastqs to output directory

type: boolean

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

type: boolean

Save unaligned sequences to output directory

type: boolean

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

type: boolean

Select aligner

hidden
type: string
default: bowtie2

Trim galore param

type: integer

Trim galore param

type: integer

Trim galore param

type: integer

Trim galore param

type: integer

Trim galore param

type: integer

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to bowtie2 index

type: string

Path to GTF annotation file

type: string

Path to genome blacklist

type: string

Name of the igenome reference for the spike-in genome

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)?$

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

Filter reads below a q-score threshold

type: integer

Deduplicate non-control reads

type: boolean

Normalisation constant

hidden
type: integer
default: 10000

Specifies if the samplesheet contains an IgG control

type: boolean
default: true

Threshold for peak calling when no IgG is present

type: number
default: 0.05

Path to gene bed file

type: string

Minimum number of overlapping replicates needed for a consensus peak

type: integer
default: 1

Run pipeline up to reference preparation

type: boolean

Run pipeline up to input checking

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 scalefactor normalisation

type: boolean

Skips reporting

type: boolean

Skips igv session generation

type: boolean

Skips deeptools heatmaps

type: boolean

Skips multiqc

type: boolean

Skip upset plot calculation

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.

hidden
type: boolean

Method used to save pipeline results to output directory.

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

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

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean

Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.

hidden
type: boolean