Whether the pipeline should only perform quality control, and skip assembly and quantification.

type: boolean

Whether the pipeline should skip assembly steps, and only perform quality control of reads and quantification. —transcript_fasta must be provided if True.

type: boolean

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 storage on Cloud infrastructure.

required
type: string

Path to fasta file (not compressed) containing a transcriptome assembly. Only needed if --skip_assembly is True.

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

File in FASTA format containing possible adapters to remove. Accepted formats: *.{fasta,fna,fas,fa}

type: string

Specify true to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz

type: boolean

Specify true to save all merged reads to the a file ending in *.merged.fastq.gz

type: boolean

Skip the fastp process if true

type: boolean

Skip FastQC processes if true

type: boolean

Extra arguements for fastp. For example, --trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5

type: string

Enable the removal of reads derived from ribosomal RNA using SortMeRNA.

type: boolean

Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.

type: string
default: ${projectDir}/assets/rrna-db-defaults.txt

If this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.

type: boolean

Assemblers to use. Possible options include trinity, trinity_no_norm (trinity without normalized reads), and rnaspades.

type: string
default: trinity,rnaspades

Extra arguments to pass to Trinity command in addition to defaults. Applies to both trinity and trinity_no_norm.

type: string

Include hard filtered transcripts (in addition to medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.

type: boolean

Include soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds.

type: boolean

Set strand-specific type for rnaSPAdes. Use rf when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and fr otherwise (forward).

type: string

Extra arguments for tr2aacds.pl. For example, ‘-MINAA=20’

type: string

The mode to run BUSCO in. One of genome, proteins, or transcriptome

type: string

The BUSCO lineage to use, or auto to automatically select lineage

type: string
default: auto

Path to local BUSCO lineages directory.

type: string

Path to BUSCO config file.

type: string

Path to FASTA genome file.

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

File with gene coordinates in GTF/GFF format (needs information about parent relations). rnaQUAST authors recommend to use files downloaded from GENCODE or Ensembl.

type: string

Path to FASTA file of reference set of proteins or transcripts from a related species

type: string

Override library type inferred based on strandedness defined in meta object. A for auto.

type: string
default: A

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

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

hidden
type: string

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean