Introduction Usage Parameters Output Releases

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$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See usage docs.

Path to comma-separated file containing information about the contrasts in the experiment.

required
type: string

Source of input files.

required
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

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

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

type: boolean

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Path to FASTA genome file.

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

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

Path to GTF annotation file.

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

This parameter is mandatory if --genome is not specified.

Path to GFF3 annotation file.

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

This parameter must be specified if --genome or --gtf are not specified.

Path to FASTA transcriptome file.

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

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

type: string

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

type: string

Specify if your transcript FASTA file is in GENCODE format.

type: boolean

If your file is in GENCODE format and you would like to run Salmon i.e. --pseudo_aligner salmon, you will need to provide this parameter in order to build the Salmon index appropriately.

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

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

type: boolean

If an alignment index is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times.

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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

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

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

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$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

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

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

Show all params when using --help

hidden
type: boolean

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.

Options to adjust read trimming criteria.

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

type: integer

Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).

type: integer

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

type: integer

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

type: integer

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

type: integer

This enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.

Save the trimmed FastQ files in the results directory.

type: boolean

Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.

type: boolean

Skip TrimGalore! FastQC.

type: boolean

Minimum number of trimmed reads below which samples are flagged in multiqc output.

type: integer
default: 10000

Defube QC options required for the workflow.

Skip FastQC.

type: boolean

Skip bigWig file creation.

type: boolean
default: true

Options to adjust parameters and filtering criteria for read alignments.

Specifies the alignment algorithm to use - available options are 'star_salmon', or 'star'.

type: string

Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'.

type: string

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

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

type: string

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

type: boolean

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

type: boolean

Save the intermediate BAM files from the alignment step.

type: boolean

By default, intermediate BAM files will not be saved. The final BAM files created after the appropriate filtering step are always saved to limit storage usage. Set this parameter to also save other intermediate BAM files.

Run Leafcutter annotation workflow.

type: boolean

Run rMATS workflow.

type: boolean

The cutoff used in the null hypothesis test for differential splicing.

type: number
default: 0.0001

Use paired statistical model.

type: boolean
default: true

The length of each read.

type: integer
default: 40

Detect splicing events that involve an unannotated splice site.

type: boolean

Minimum Intron Length.

type: integer
default: 50

Maximum exon length.

type: integer
default: 500

Run DEXSeq differential exon usage workflow.

type: boolean

Save pre-processed GFF annotation file.

type: boolean

Path to GFF3 annotation file.

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

Minimum alignment quality required for reads to be counted.

type: integer
default: 10

Combine overlapping genes into a single aggregate gene.

type: boolean
default: true

Save plots of the per gene DEXSeq results.

type: boolean
default: true

Plot the N most significant genes from the DEXSeq results.

type: integer
default: 10

Run edgeR workflow.

type: boolean

Save plots of the per gene edgeR results.

type: boolean
default: true

Plot the N most significant genes from the edgeR results.

type: integer
default: 10

Run DEXSeq differential transcript usage workflow.

type: boolean

Generate estimated counts using dtuScaledTPM or scaledTPM abundance estimates.

type: string

Minimal number of samples where genes should be expressed.

type: integer
default: 4

Minimal number of samples where features should be expressed.

type: integer
default: 2

Minimal proportion of samples where features should be expressed.

type: integer
default: 2

Minimal gene expression.

type: integer
default: 10

Minimal feature expression.

type: integer
default: 10

Minimal proportion for feature expression. This value should be between 0 and 1.

type: number
default: 0.1

Create sashimi plots using MISO.

type: boolean

List containing identifiers of genes to plot.

type: string
default: ENSG00000004961, ENSG00000005302, ENSG00000147403
pattern: ^[\w-]+(,\s+[\w-]+)*$

New-line separate file containing identifiers of genes to plot.

type: string

Read length used to calculate coverage.

type: integer
default: 75

Sashimi figure height (inches).

type: integer
default: 7

Sashimi figure width (inches).

type: integer
default: 7

Run SUPPA workflow.

type: boolean
default: true

Quantify event inclusion levels (PSIs) from multiple samples.

type: boolean
default: true

Quantify isoform inclusion levels (PSIs) from multiple samples.

type: boolean
default: true

Expression file containing the abundances of all transcripts (ideally in TPM units).

type: string

An example can be found at "${projectDir}/assets/tpm.txt"

Redefine genes by clustering together transcripts by genomic stranded overlap and sharing at least one exon.

type: boolean
default: true

Space separated list of events to generate.

type: string
default: SE SS MX RI FL

Boundary type (only used for local AS events).

type: string

Variability treshold.

type: integer
default: 10

Defines the number of nucleotides to display in the output GTF.

type: integer
default: 100

Minimum total expression of the transcripts involved in the event.

type: integer

Calculate differential splicing for AS events across multiple conditions with replicates.

type: boolean
default: true

Calculate differential splicing for differential transcript usage across multiple conditions with replicates

type: boolean
default: true

The method to use to calculate the significance.

type: string

Integer indicating the number of points in the local area of the delta PSI - average TPM distribution.

type: integer
default: 1000

Lower-bound for the absolute delta PSI value to test for significance.

type: integer

Correct the p-values by gene.

type: boolean
default: true

Indicates if replicates across conditions are paired.

type: boolean
default: true

Family-wise error rate to use for the multiple test correction.

type: number
default: 0.05

Use the median to calculate the Delta PSI, instead of the mean.

type: boolean

Minimum expression (calculated as average TPM value within-replicates and between-conditions) to be included in the analysis.

type: integer

Proportion of samples with nan values allowed per condition to calculate a DeltaPSI .

type: integer

Cluster events according to PSI values across conditions

type: boolean
default: true

Cluster transcripts according to PSI values across conditions

type: boolean
default: true

P-value threshold to consider an event significant from the dpsi file.

type: number

Lower-bound for the absolute delta PSI value to cluster.

type: number
default: 0.05

Maximum distance (between 0 and 1) to consider two events as members of the same cluster.

type: number
default: 0.05

Distance metric.

type: string

Maximum distance in PSI space of an event to a cluster.

type: integer

Minimum number of events required per cluster.

type: integer
default: 20

Clustering method to use (DBSCAN, OPTICS).

type: string
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