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

]

`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

]

`*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

]

`*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

]

`*comp.csv:file`

An optional (dis)similarity matrix in CSV format

*.comp.csv

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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`

`versions.yml:file`

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

versions.yml:file

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`

`versions.yml:file`

sourmash
BSD-3-clause