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Add skani round 2 #5539

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Add skani round 2 #5539

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3f53b60
Added skani modules
CarsonJM Apr 18, 2024
0978c53
Prettier
CarsonJM Apr 18, 2024
ea66cc0
Merge branch 'add-skani' of https://github.com/CarsonJM/modules into …
CarsonJM Apr 29, 2024
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7 changes: 7 additions & 0 deletions modules/nf-core/skani/dist/environment.yml
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name: "skani_dist"
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- "bioconda::skani=0.2.1"
50 changes: 50 additions & 0 deletions modules/nf-core/skani/dist/main.nf
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process SKANI_DIST {
tag "$meta.id"
label 'process_high'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/skani:0.2.1--h4ac6f70_0':
'biocontainers/skani:0.2.1--h4ac6f70_0' }"

input:
tuple val(meta) , path(query)
tuple val(meta2), path(reference)

output:
tuple val(meta), path("${prefix}.tsv") , emit: dist
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
"""
skani \\
dist \\
-q ${query} \\
-r ${reference} \\
-o ${prefix}.tsv \\
-t ${task.cpus} \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
skani: \$(skani --version 2>&1 | sed 's/^.*skani //; s/ .*\$//')
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
skani: \$(skani --version 2>&1 | sed 's/^.*skani //; s/ .*\$//')
END_VERSIONS
"""
}
56 changes: 56 additions & 0 deletions modules/nf-core/skani/dist/meta.yml
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name: "skani_dist"
description: Simple ANI calculation between reference and query genomes.
keywords:
- skani
- metagenomics
- genome
- alignment
- sketch
- distance
- dist
tools:
- "skani":
description: "skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs."
homepage: "https://github.com/bluenote-1577/skani"
documentation: "https://github.com/bluenote-1577/skani/wiki"
tool_dev_url: "https://github.com/bluenote-1577/skani"
doi: "10.1038/s41592-023-02018-3"
licence: ["MIT"]

input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1' ]`
- query:
type: file
description: |
FASTA/skani sketch file to be used as query.
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,sketch}"
- reference:
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Can you add meta2 here too?

type: file
description: |
FASTA/skani sketch file to be used as reference.
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,sketch}"

output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1' ]`
- dist:
type: file
description: |
TSV file containing ANI and AF between query and reference as calculated by skani.
pattern: "*.tsv"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"

authors:
- "@CarsonJM"
maintainers:
- "@CarsonJM"
130 changes: 130 additions & 0 deletions modules/nf-core/skani/dist/tests/main.nf.test
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nextflow_process {

name "Test Process SKANI_DIST"
script "../main.nf"
process "SKANI_DIST"

tag "modules"
tag "modules_nfcore"
tag "skani"
tag "skani/dist"

// Dependencies
tag "skani/sketch"

setup {
run("SKANI_SKETCH", alias: "SKANI_SKETCH1") {
script "../../sketch/main.nf"
process {
"""
input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta.gz", checkIfExists: true)
]
"""
}
}

run("SKANI_SKETCH", alias: "SKANI_SKETCH2") {
script "../../sketch/main.nf"
process {
"""
input[0] = [
[ id: 'test2' ],
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fasta/contigs.fasta", checkIfExists: true)
]
"""
}
}
}

test("fasta.gz + fasta") {
when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta.gz", checkIfExists: true)
]
input[1] = [
[ id:'test2' ], // meta map
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fasta/contigs.fasta", checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("fasta.gz + fastq - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta.gz", checkIfExists: true)
]
input[1] = [
[ id:'test2' ], // meta map
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fasta/contigs.fasta", checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("sketch + sketch") {
when {
process {
"""
input[0] = SKANI_SKETCH1.out.sketch
input[1] = SKANI_SKETCH2.out.sketch
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("sketch + sketch - stub") {

options "-stub"

when {
process {
"""
input[0] = SKANI_SKETCH1.out.sketch
input[1] = SKANI_SKETCH2.out.sketch
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
134 changes: 134 additions & 0 deletions modules/nf-core/skani/dist/tests/main.nf.test.snap
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{
"sketch + sketch": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_test2.tsv:md5,1ec6d25df7952408655bcdd7ec123600"
]
],
"1": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
],
"dist": [
[
{
"id": "test"
},
"test_test2.tsv:md5,1ec6d25df7952408655bcdd7ec123600"
]
],
"versions": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-18T19:13:41.612024778"
},
"fasta.gz + fasta": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_test2.tsv:md5,1ec6d25df7952408655bcdd7ec123600"
]
],
"1": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
],
"dist": [
[
{
"id": "test"
},
"test_test2.tsv:md5,1ec6d25df7952408655bcdd7ec123600"
]
],
"versions": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-18T19:13:15.692205997"
},
"sketch + sketch - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
],
"dist": [
[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-18T19:13:53.29278095"
},
"fasta.gz + fastq - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
],
"dist": [
[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,a8a2d2137a0a871bbd99d861ca4db12f"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-18T19:13:29.440772434"
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/skani/dist/tests/tags.yml
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skani/dist:
- "modules/nf-core/skani/dist/**"
7 changes: 7 additions & 0 deletions modules/nf-core/skani/search/environment.yml
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name: "skani_search"
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- "bioconda::skani=0.2.1"
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