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

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

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

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

Path to GTF annotation file.

type: string
pattern: ^\S+\.gtf(\.gz)?$

Path to GFF3 annotation file.

type: string
pattern: ^\S+\.gff(\.gz)?$

Path to BED file containing gene intervals. This will be created from the GTF file if not specified.

type: string
pattern: ^\S+\.bed(\.gz)?$

Path to FASTA transcriptome file.

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

FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences.

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

Splice sites file required for HISAT2.

type: string

Path to directory or tar.gz archive for pre-built STAR index.

type: string

Path to directory or tar.gz archive for pre-built HISAT2 index.

type: string

Path to directory or tar.gz archive for pre-built RSEM index.

type: string

Path to directory or tar.gz archive for pre-built Salmon index.

type: string

Path to directory or tar.gz archive for pre-built Kallisto index.

type: string

Minimum memory required to use splice sites and exons in the HiSAT2 index build process.

type: string
default: 200.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Specify if your GTF annotation is in GENCODE format.

type: boolean

By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.

type: string
default: gene_name

Define the attribute type used to group features in the GTF file when running Salmon.

type: string
default: gene_id

The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts.

type: string
default: gene_biotype

By default, the pipeline assigns reads based on the ‘exon’ attribute within the GTF file.

type: string
default: exon

Do not load the iGenomes reference config.

hidden
type: boolean

The base path to the igenomes reference files

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

Options to adjust read trimming criteria.

Specifies the trimming tool to use - available options are ‘trimgalore’ and ‘fastp’.

type: string

Extra arguments to pass to Trim Galore! command in addition to defaults defined by the pipeline.

type: string

Extra arguments to pass to fastp command in addition to defaults defined by the pipeline.

type: string

Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.

type: integer
default: 10000

Options for filtering reads prior to alignment

Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit. You have to also explicitly set --skip_bbsplit false if you want to use BBSplit.

type: string

Path to directory or tar.gz archive for pre-built BBSplit index.

type: string

Path to directory or tar.gz archive for pre-built sortmerna index.

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}/workflows/rnaseq/assets/rrna-db-defaults.txt

Options for processing reads with unique molecular identifiers

Enable UMI-based read deduplication.

type: boolean

UMI pattern to use. Can be either ‘string’ (default) or ‘regex’.

type: string
default: string

The UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.

type: string

The UMI barcode pattern to use if the UMI is located in read 2.

type: string

After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.

type: integer

The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software.

type: string

Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying the reads with the same mapping position, but treat similar yet nonidentical UMIs differently.

type: string

Generate output stats when running “umi_tools dedup”.

type: boolean

Options to adjust parameters and filtering criteria for read alignments.

Specifies the alignment algorithm to use - available options are ‘star_salmon’, ‘star_rsem’ and ‘hisat2’.

type: string

Specifies the pseudo aligner to use - available options are ‘salmon’. Runs in addition to ‘—aligner’.

type: string

Kmer length passed to indexing step of pseudoaligners

type: integer
default: 31

Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.

type: boolean

When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file.

type: boolean

Override Salmon library type inferred based on strandedness defined in meta object.

type: string

Minimum percentage of uniquely mapped reads below which samples are removed from further processing.

type: number
default: 5

Sequencing center information to be added to read group of BAM files.

type: string

Perform reference-guided de novo assembly of transcripts using StringTie i.e. dont restrict to those in GTF file.

type: boolean

Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline. Only available for the STAR-Salmon route.

type: string

Extra arguments to pass to Salmon quant command in addition to defaults defined by the pipeline.

type: string

Extra arguments to pass to Kallisto quant command in addition to defaults defined by the pipeline.

type: string

In single-end mode Kallisto requires an estimated fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.

type: integer
default: 200

In single-end mode, Kallisto requires an estimated standard error for fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.

type: integer
default: 200

The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5.

type: number
default: 0.8

The difference in fraction of stranded reads assigned to ‘forward’ and ‘reverse’ below which a sample is classified as ‘unstranded’. By default the forward and reverse fractions must differ by less than 0.1 for the sample to be called as unstranded.

type: number
default: 0.1

Additional output files produces as intermediates that can be saved

Save FastQ files after merging re-sequenced libraries in the results directory.

type: boolean

If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.

type: boolean

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

type: boolean

If this option is specified, FastQ files split by reference will be saved in the results directory.

type: boolean

If generated by the pipeline save the STAR index in the results directory.

type: boolean

Save the trimmed FastQ files in the results directory.

type: boolean

Save the intermediate BAM files from the alignment step.

type: boolean

Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.

type: boolean

Save read-by-read assignments from Kraken2.

type: boolean

Save reads that were not given assignment from Kraken2.

type: boolean

Additional quality control options.

Use vst transformation instead of rlog with DESeq2.

type: boolean
default: true

Specify the RSeQC modules to run.

type: string
default: bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication

Tool to use for detecting contaminants in unaligned reads - available options are ‘kraken2’ and ‘kraken2_bracken’

type: string

Database when using Kraken2/Bracken for contaminant screening.

type: string

Taxonomic level for Bracken abundance estimations.

type: string

Options to skip various steps within the workflow.

Skip filtering of GTF for valid scaffolds and/ or transcript IDs.

type: boolean

Skip the ‘transcript_id’ checking component of the GTF filtering script used in the pipeline.

type: boolean

Skip BBSplit for removal of non-reference genome reads.

type: boolean
default: true

Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run.

type: boolean

Skip the adapter trimming step.

type: boolean

Skip all of the alignment-based processes within the pipeline.

type: boolean

Skip all of the pseudoalignment-based processes within the pipeline.

type: boolean

Skip picard MarkDuplicates step.

type: boolean

Skip bigWig file creation.

type: boolean

Skip StringTie.

type: boolean

Skip FastQC.

type: boolean

Skip Preseq.

type: boolean
default: true

Skip dupRadar.

type: boolean

Skip Qualimap.

type: boolean

Skip RSeQC.

type: boolean

Skip additional featureCounts process for biotype QC.

type: boolean

Skip DESeq2 PCA and heatmap plotting.

type: boolean

Skip MultiQC.

type: boolean

Skip all QC steps except for MultiQC.

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

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/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/