modules/sourmash_compare

Compare many FracMinHash signatures generated by sourmash sketch.

compareFracMinHash sketchcontainmentsourmashmetagenomicsgenomicskmer

https://github.com/nf-core/modules/[...]/modules/nf-core/sourmash/compare

Description

Compare many FracMinHash signatures generated by sourmash sketch.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`signatures`
`:file`

Files containing signatures (hash sketches) of samples

*.{sig}

`file_list`
`:file`

An optional file specifying a list of file paths that should be appended to the input signatures.

`save_numpy_matrix`
`:boolean`

If true, output will contain a (dis)similarity matrix numpy binary format. At least one of save_numpy_matrix or save_csv is required.

`save_csv`
`:boolean`

If true, output will contain a (dis)similarity matrix in CSV format At least one of save_numpy_matrix or save_csv is required.

Output

name:type

description

pattern

`matrix`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*comp.npy`
`:file`

An optional (dis)similarity matrix numpy binary format

*.comp

`labels`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*comp.npy.labels.txt`
`:file`

A text file that specifies the labels in the output numpy_matrix

*.comp.labels.txt

`csv`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*comp.csv`
`:file`

An optional (dis)similarity matrix in CSV format

*.comp.csv

`versions_sourmash`

`${task.process}`
`:string`

The name of the process

`sourmash`
`:string`

The name of the tool

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`sourmash`
`:string`

The name of the tool

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

The expression to obtain the version of the tool

Tools

sourmash
BSD-3-clause

Compute and compare FracMinHash signatures for DNA and protein data sets.

sourmash.readthedocs.io https://github.com/sourmash-bio/sourmash 10.21105/joss.00027

modules/sourmash_compare

Description

Input

`meta`
`:map`

`signatures`
`:file`

`file_list`
`:file`

`save_numpy_matrix`
`:boolean`

`save_csv`
`:boolean`

Output

`matrix`

`meta`
`:map`

`*comp.npy`
`:file`

`labels`

`meta`
`:map`

`*comp.npy.labels.txt`
`:file`

`csv`

`meta`
`:map`

`*comp.csv`
`:file`

`versions_sourmash`

`${task.process}`
`:string`

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

Tools

sourmash
BSD-3-clause

included in

maintainer

get in touch

modules/sourmash_compare

Description

Input

meta:map

signatures:file

file_list:file

save_numpy_matrix:boolean

save_csv:boolean

Output

matrix

meta:map

*comp.npy:file

labels

meta:map

*comp.npy.labels.txt:file

csv

meta:map

*comp.csv:file

versions_sourmash

${task.process}:string

sourmash:string

sourmash --version 2>&1 | sed 's/^sourmash //':eval

Topics

versions

${task.process}:string

sourmash:string

sourmash --version 2>&1 | sed 's/^sourmash //':eval

Tools

sourmash BSD-3-clause

included in

maintainer

get in touch

`meta`
`:map`

`signatures`
`:file`

`file_list`
`:file`

`save_numpy_matrix`
`:boolean`

`save_csv`
`:boolean`

`matrix`

`meta`
`:map`

`*comp.npy`
`:file`

`labels`

`meta`
`:map`

`*comp.npy.labels.txt`
`:file`

`csv`

`meta`
`:map`

`*comp.csv`
`:file`

`versions_sourmash`

`${task.process}`
`:string`

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

`versions`

`${task.process}`
`:string`

`sourmash`
`:string`

`sourmash --version 2>&1 | sed 's/^sourmash //'`
`:eval`

sourmash
BSD-3-clause