Define where the pipeline should find input data and save output data.

Path to fastq.gz files in quotes

type: string

Test paths for input reads

hidden
type: string

Test paths for fastas

hidden
type: string

Test paths for protein fastas

hidden
type: string

Path to Local or s3 directories containing R1,R2.fastq.gz files, separated by commas.

type: string

Path to Local or s3 directories of single-end read files, separated by commas.

type: string

CSV file with columns id, read1, read2 for each sample

type: string

CSV file with columns id, read1, for each sample

type: string

Path to FASTA sequence files. Can be semi-colon-separated.

type: string

Path to protein fasta inputs.

type: string

Path to bam input.

type: string

Path to input tgz folder containing bam and bai files.

type: string

SRR, ERR, SRP IDs representing a project. Only compatible with Nextflow 19.03-edge or greater

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.

Path to the output directory where the results will be saved.

type: string

Sketch size options for sourmash compute

Number of hashes to use for making the sketches. Mutually exclusive with --sketch_num_hashes_log2

type: integer

Which log2 sketch sizes to use. Multiple are separated by commas. Mutually exclusive with --sketch_num_hashes

type: integer

Observe every 1/N hashes per sample, rather than a flat rate of N hashes per sample. This way, the number of hashes scales by the sequencing depth. Mutually exclusive with --sketch_scaled_log2

type: integer

Same as --sketch_scaled, but instead of specifying the true number of hashes, specify the power to take 2 to. Mutually exlusive with --sketch_scaled

type: integer

Options for kmer computation

Track abundance of each hashed k-mer, could be useful for cancer RNA-seq or ATAC-seq analyses

type: boolean

If provided, use SKA to compute split k-mer sketches instead of sourmash to compute k-mer sketches

type: boolean

Which nucleotide k-mer sizes to use. Multiple are separated by commas

type: string
default: '21,27,33,51'

dna,protein,dayhoff

type: string

Integer value to subsample reads from input fastq files

type: integer

Options to translate RNA-seq reads into protein-coding sequences .

Path to a well-curated fasta file of protein sequences. Used to filter for coding reads

type: string

K-mer size to use for translating RNA into protein, which is good for 'protein'. If using dayhoff, suggest 15

type: integer
default: 9

Which molecular encoding to use for translating.If your reference proteome is quite different from your species of interest, suggest using dayhoff

type: string
default: protein

Minimum fraction of overlapping translated k-mers from the read to match to the reference.

type: string
default: 0.95

Maximum table size for bloom filter creation

type: integer

Remove ribosomal RNA with SortMeRNA

If on, removes ribosomal RNA

type: boolean

Save non ribosomal rna reads if true

type: boolean

Path to rrna database manifest txt file

type: string

Options to adjust parameters and filtering criteria for read alignments.

A barcode is only considered a valid barcode read and its signature is written if number of umis are greater than tenx_min_umi_per_cell

type: integer

For bam files, Optional absolute path to a .tsv barcodes file if the input is unfiltered 10x bam file

type: string

For bam files, Optional absolute path to a .tsv Tab-separated file mapping 10x barcode name to new name, e.g. with channel or cell annotation label

type: string

For bam files, Csv file name relative to outdir/barcode_metadata to write number of reads and number of umis per barcode. This csv file is empty with just header when the tenx_min_umi_per_cell is zero i.e Reads and umis per barcode are calculated only when the barcodes are filtered based on tenx_min_umi_per_cell

type: string

Path to single barcode save the fastas inside the output directory where the results will be saved.

type: string

10x sam tags

type: string

10x Cell pattern

type: string

10x UMI pattern

type: string

Options to skip various steps within the workflow.

Skip fastp trimming of reads

type: boolean

Skip sourmash compute.

type: boolean

Skip sourmash compare.

type: boolean

Skip merging aligned+unaligned reads per cell (keep aligned/unaligned separate)

type: boolean

Skip 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

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 configs hostname.

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

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

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

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.

Workflow name.

hidden
type: string

A custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.

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

Do not use coloured log outputs.

hidden
type: boolean

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info