5. Inputs

Overview

Pipeline parameters can be adjusted using the following methods:

1. At the command line using --{parameter_name} (e.g., --input)
2. In the nextflow.config file
3. In a JSON file via the -params-file parameter

It is also possible pass arguments directly to a pipeline process using the ext.args variable in conf/modules.config (see example below):

    withName: 'CONDENSE' {
        ext.args            = ""
        ext.when            = {  }
        publishDir = [
            [
                path: { "${params.outdir}/${taxon}" },
                pattern: "none",
                mode: 'copy'
            ]
    }

Input Options

--input

Path to the samplesheet.

Example samplesheet

samplesheet.csv:

taxon,segmented,segmentSynonyms
Hantavirus,TRUE,s|small;m|medium|middle;l|large
Norovirus,FALSE,

Description of Columns

Column Name	Description
taxon	The taxon name. This must be the taxId name used by NCBI if using --ncbi true.
segmented	If the genome is segmented (TRUE or FALSE).
segment	The segment name. This is only needed if you are supplying sequence and/or sample data.
segmentSynonyms	Accepted segment names and their synonyms. Segments are separated by a semicolon (;). Synonyms are separated by a pipe (`
assembly	Path to a multi-FASTA file containing input sequence.
metadata	Path to a CSV file containing sample data about the input sequence.

--dist_threshold

The distance threshold used to create references: 1 - [ % ANI / 100 ].

• Options: 0...1
• Default: 0.02

--len_threshold

The sequence length threshold used to filter input sequences: length +- len_threshold*mean(length)

• Options: 0...1
• Default: 0.20

--amb_threshold

The ratio of ambiguous bases (N) allowed in a sequence.

• Options: 0...1
• Default: 0.02

--max_cluster

Maximum number of sequences to include in hierarchal clustering.

• Options: 0...Inf
• Default: 1000

Caution

Increasing this value can significantly increase run time and may cause the pipeline to fail.

--max_align

Maximum number of sequences to include in an alignment.

• Options: 0...Inf
• Default: 1000

Note

Sequences are randomly subsampled to this value within each cluster.

Caution

Increasing this value can significantly increase run time and may cause the pipeline to fail.

--ksize

K-mer size used when calculating average nucleotide identity using Sourmash (for clustering and condensing).

• Options: ?...?
• Default: 31

Note

Options are whatever Sourmash allows 🙈

--scaled

Scaled value used by Sourmash when calculating average nucleotide identity (for clustering and condensing).

• Options: 0...?
• Default: 1000

Note

Options are whatever Sourmash allows 🙈

--ncbi

Automatically pull data from NCBI for the taxId name specified in the taxon column.

• Options: true or false
• Default: true

--create

Create reference set.

• Options: true or false
• Default: true

Note

This option is useful if you want to make adjustments to the input sequences prior to reference selection. In this case, you would first run the pipeline with --create false --ncbi true and then run again with --ncbi false --create true using the modified datasets, supplied via the assembly and metadata columns.