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

Only a parameter added to avoid warning as per nf-core

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})$

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

Number of alignment to contain in each sharded bam file

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 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 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

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

hidden
type: string
default: 128.GB

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

hidden
type: string
default: 240.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

Workflow name.

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

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

Arguments passed to Nextflow clusterOptions.

hidden
type: string

Run this workflow with Conda.

hidden
type: boolean

Test paths for input reads

hidden
type: string

Test paths for fastas

hidden
type: string

Test paths for protein fastas

hidden
type: string