Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

try porting mmseqs/search to nf-test #7231

Merged
merged 10 commits into from
Jan 15, 2025
+199 −69
Merged

try porting mmseqs/search to nf-test #7231

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
4381c1b
try porting to nf-test
famosab Dec 17, 2024
603ffd5
remove from pytest
famosab Dec 17, 2024
4812b52
Apply suggestions from code review
famosab Dec 19, 2024
39bf174
fix stub
famosab Dec 19, 2024
f6bdfb0
remove pytest
famosab Dec 19, 2024
b628d0c
Merge branch 'master' into search
famosab Dec 19, 2024
e2f2bd1
Working except for linting
SPPearce Jan 15, 2025
6f638f4
Only check the names
SPPearce Jan 15, 2025
7f46401
Merge branch 'master' into search
SPPearce Jan 15, 2025
ae2ceae
Fix meta for linting
SPPearce Jan 15, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 1 addition & 4 deletions modules/nf-core/mmseqs/easysearch/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,11 +47,8 @@ process MMSEQS_EASYSEARCH {
"""

stub:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: "*.dbtype"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
${prefix}.tsv
touch ${prefix}.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
16 changes: 6 additions & 10 deletions modules/nf-core/mmseqs/search/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,18 @@

process MMSEQS_SEARCH {
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/mmseqs2:14.7e284--pl5321h6a68c12_2':
'biocontainers/mmseqs2:14.7e284--pl5321h6a68c12_2' }"
'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0':
'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }"

input:
tuple val(meta), path(db_query)
tuple val(meta2), path(db_target)

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

when:
Expand All @@ -40,9 +39,7 @@ process MMSEQS_SEARCH {
${prefix}/${prefix} \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1

--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -51,8 +48,7 @@ process MMSEQS_SEARCH {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
if ("$db_query" == "${prefix}" || "$db_target" == "${prefix}" ) error "Input and output names of databases are the same, set prefix in module configuration to disambiguate!"
"""
mkdir -p $prefix
Expand All @@ -62,7 +58,7 @@ process MMSEQS_SEARCH {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mmseqs: \$(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: /')
mmseqs: \$(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //')
END_VERSIONS
"""
}
2 changes: 1 addition & 1 deletion modules/nf-core/mmseqs/search/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ output:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
- ${prefix}:
- ${prefix}/:
type: directory
description: an MMseqs2 database with search results
- versions:
Expand Down
95 changes: 95 additions & 0 deletions modules/nf-core/mmseqs/search/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,95 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "mmseqs"
tag "mmseqs/search"
tag "mmseqs/createdb"

config "./nextflow.config"

setup {
run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_QUERY") {
script "../../../mmseqs/createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_query', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
]
"""
}
}

run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_TARGET") {
script "../../../mmseqs/createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_target', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
]
"""
}
}
}

test("sarscov2 - test-search") {

when {
params {
module_args = '--remove-tmp-files 1 --search-type 2'
module_prefix = 'test_output_search'
}
process {
"""
input[0] = MMSEQS_CREATEDB_QUERY.out.db
input[1] = MMSEQS_CREATEDB_TARGET.out.db
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.db_search.get(0).get(1)).list().sort(), //second file is empty so fails linting
jfy133 marked this conversation as resolved.
Show resolved Hide resolved
path(process.out.versions[0]).yaml
).match() }
)
}

}

test("sarscov2 - test-search - stub") {

options "-stub"

when {
params {
module_args = '--remove-tmp-files 1 --search-type 2'
module_prefix = 'test_output_search'
}
process {
"""
input[0] = MMSEQS_CREATEDB_QUERY.out.db
input[1] = MMSEQS_CREATEDB_TARGET.out.db
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}

}

}
88 changes: 88 additions & 0 deletions modules/nf-core/mmseqs/search/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
{
"sarscov2 - test-search": {
"content": [
[
"test_output_search.0",
"test_output_search.1",
"test_output_search.dbtype",
"test_output_search.index"
],
{
"MMSEQS_SEARCH": {
"mmseqs": "15.6f452"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-15T09:38:30.159081322"
},
"sarscov2 - test-search - stub": {
"content": [
{
"0": [
[
{
"id": "test_query",
"single_end": true
},
[
"test_output_search.0:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.1:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.2:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.3:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.4:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.5:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.6:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.7:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.8:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.9:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.index:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
"versions.yml:md5,2568126b1f8eb47999b31cd5f3b9c68e"
],
"db_search": [
[
{
"id": "test_query",
"single_end": true
},
[
"test_output_search.0:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.1:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.2:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.3:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.4:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.5:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.6:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.7:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.8:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.9:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.index:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,2568126b1f8eb47999b31cd5f3b9c68e"
]
},
{
"MMSEQS_SEARCH": {
"mmseqs": "15.6f452"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-15T09:28:46.406630911"
}
}
8 changes: 8 additions & 0 deletions modules/nf-core/mmseqs/search/tests/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
process {

withName: MMSEQS_SEARCH {
ext.prefix = params.module_prefix
ext.args = params.module_args
}

}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -323,9 +323,6 @@ mitohifi/mitohifi:
mmseqs/easysearch:
- modules/nf-core/mmseqs/easysearch/**
- tests/modules/nf-core/mmseqs/easysearch/**
mmseqs/search:
- modules/nf-core/mmseqs/search/**
- tests/modules/nf-core/mmseqs/search/**
mmseqs/tsv2exprofiledb:
- modules/nf-core/mmseqs/tsv2exprofiledb/**
- tests/modules/nf-core/mmseqs/tsv2exprofiledb/**
Expand Down
23 changes: 0 additions & 23 deletions tests/modules/nf-core/mmseqs/search/main.nf
View file
Open in desktop

This file was deleted.

17 changes: 0 additions & 17 deletions tests/modules/nf-core/mmseqs/search/nextflow.config
View file
Open in desktop

This file was deleted.

11 changes: 0 additions & 11 deletions tests/modules/nf-core/mmseqs/search/test.yml
View file
Open in desktop

This file was deleted.

Loading