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$

Activate when using single end reads input

type: boolean

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

required
type: string

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

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 (paired-end reads only).

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

Save the trimmed FastQ files in the results directory.

type: boolean

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

type: string

Skip the adapter trimming step.

type: boolean

Fasta file with sequences to filter away before running assembly etc..

type: string

Save the resulting fastq files from filtering

type: boolean
default: false

Use these option if you need to normalize the reads before the assembly

Perform normalization to reduce sequencing depth.

type: boolean

Reduce the number of reads for assembly average coverage of this number.

type: integer
default: 100

Reads with an apparent depth of under nx will be presumed to be errors and discarded

type: integer
default: 5

Save the resulting fastq files from normalization

type: boolean
default: false

Specify the assembler to run. Possible alternatives: megahit, spades.

type: string

Path to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.

type: string

Name to give to the user-provided assembly.

type: string
default: user_assembly

Filter out contigs shorter than this.

type: integer

Select which type of assembly you want to make. Default: rna

type: string

Save the formatted spades fasta file

type: boolean

Save the bam files from mapping

type: boolean

Save the output from samtools

type: boolean
default: true

Minimum identity needed to assign read to a contig

type: number
default: 0.9

Specify which ORF caller to run. Possible alternatives: prodigal, prokka, transdecoder. This needs to be set unless the --user_orfs_* params are set.

type: string

Path to a protein fasta file for user-provided ORFs.

type: string

Path to a gff file for user-provided ORFs.

type: string

Name to give to user-provided ORFs.

type: string
default: user_orfs

Specify a training file for prodigal. By default prodigal will learn from the input sequences

type: string

Size of individual files annotated by Prokka in one batch.

hidden
type: string
default: 10 MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Skip EGGNOG functional annotation

type: boolean

Specify EGGNOG database path

type: string
default: eggnog

If enabled, skips the run of KofamScan.

type: boolean

Path to a directory with KOfam files. Will be created if it doesn’t exist.

type: string
default: ./kofam/

Directory with hmm files which will be searched for among ORFs

type: string
pattern: ^\S+

Comma-separated list of hmm files which will be searched for among ORFs

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

Specify which pattern hmm files end with

type: string
default: *.hmm

Path to comma-separated file containing information about Diamond database files you want to use for taxonomy assignment.

type: string
pattern: ^\S+\.(csv|tsv|json|yaml|yml)$

Argument to Diamond’s --top that controls the percentage of hits to include in the LCA.

type: integer
default: 10

If enabled, skips the run of EUKulele

type: boolean

Specify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets

type: string

EUKulele database.

type: string

EUKulele database folder.

type: string
default: ./eukulele/

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