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

Path to fastq input files

required
type: string

path/to/kraken2_db_dir

type: string

Path to sourcepredict labels file

type: string
default: /Users/maxime/Documents/github/coproid/data/sourcepredict/modern_gut_microbiomes_labels.csv

Path to sourcepredict sources file

type: string
default: /Users/maxime/Documents/github/coproid/data/sourcepredict/modern_gut_microbiomes_sources.csv

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 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

Name of candidate species 1

type: string

Name of candidate species 2

type: string

Name of candidate species 3

type: string

iGenome name for target genome 1

type: string

iGenome name for target genome 2

type: string

iGenome name for target genome 3

type: string

Path to Bowtie2 pre-indexed genome candidate 1

type: string

Path to Bowtie2 pre-indexed genome candidate 2

type: string

Path to Bowtie2 pre-indexed genome candidate 3

type: string

Fasta reference of genome candidate 1

type: string

Fasta reference of genome candidate 2

type: string

Fasta reference of genome candidate 3

type: string

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

Display help text.

hidden
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

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

Name of pipeline run

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*)+$

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

Specifies that the input is single-end reads.

type: boolean

Specifies if AdapterRemoval should merge the paired-end sequences or not.

type: string
default: true

Phred quality encoding

type: integer

Identity threshold to retain read alignment.

type: number
default: 0.95

Specifies if data is modern (false) or ancient DNA (true).

type: string
default: true

Minimum PMDscore to retain read alignment.

type: integer
default: 3

DNA preparation library type

type: string

Bowtie settings for sensivity

type: string

Minimum number of Kraken hits per Taxonomy ID to report

type: integer
default: 50

Proportion of Endogenous DNA in organism 1 target microbiome

type: number
default: 0.01

Proportion of Endogenous DNA in organism 2 target microbiome

type: number
default: 0.01

Proportion of Endogenous DNA in organism 3 target microbiome

type: number
default: 0.01

Sourcepredict normalization method

type: string
default: gmpr

Sourcepredict number of embedding dimenstions

type: integer
default: 2

Sourcepredict embedding method

type: string
default: mds

Sourcepredict number of neighbours

type: string
default: all