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 comma-separated file containing information about the genomes to be mapped to.

type: string

Path to comma-separated file containing a .tsv file which has the same columns as the output from GTDB-Tk. (see docs)

type: string

Path to txt file with information about genomes in NCBI.

type: string
default: ./assets/ncbi_genome_infos.csv

Path to .sbt file.

type: string

Path to comma-separated file containing information from GTDB. For column description, see docs.

type: string

Path to comma-separated file containing the output from CheckM. For column description, see docs.

type: string

Activate when you work with single ends reads.

type: boolean

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

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

required
type: string

Option for QC steps

Skip all QC steps except for MultiQC.

type: boolean

Skip FastQC.

type: boolean

All the trim option are listed below

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

type: string

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

type: string

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

type: string

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

type: string

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

type: string

Save the trimmed FastQ files in the results directory.

type: boolean

Skip the adapter trimming step.

type: boolean

All the options you can use for BBmap or BBduk)

Instructs BBduk to use a fasta file to filter away sequences before running further analysis.

type: string

Minimal identity for BBmap

type: number
default: 0.9

Save bam output file

type: boolean

Save ref folder containing the reference index

type: boolean

Save genomes concatenated file

type: boolean

Prokka option

Enable to save prokka output. Default: false

type: boolean

FeatureCounts option

Specify which features to count

type: string
default: CDS,rRNA,tRNA,tmRNA

All the options available for Sourmash

Activate Sourmash

type: boolean

K-mer size used by Sourmash

type: integer
default: 21

Save Sourmash outuput

type: boolean

Saves query sequences that do not have a match in the database, allowing further analysis of unclassified data.

type: boolean
default: true

Stores all database signatures that matched the query, enabling reuse without re-running the search.

type: boolean
default: true

Saves prefetched signatures, which are database entries that share similarity with the query but may not be full matches, for further inspection.

type: boolean
default: true

Outputs a CSV file summarizing the prefetched results, including metadata about retrieved signatures.

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

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

Display version and exit.

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

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

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string