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Foldseek: createdb and easysearch modules version bump + stub nf-tests added #5906

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merged 4 commits into from
Jul 2, 2024
Merged

Foldseek: createdb and easysearch modules version bump + stub nf-tests added #5906

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2e27bf1
foldseek/createdb version bump, added stub nf-test
vagkaratzas Jul 2, 2024
d4ac7df
foldseek/easysearch version bump, stub nf-test added
vagkaratzas Jul 2, 2024
3d004c3
test.snap for createdb added
vagkaratzas Jul 2, 2024
6dc4b4e
Merge branch 'master' into foldseek
vagkaratzas Jul 2, 2024
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3 changes: 2 additions & 1 deletion modules/nf-core/foldseek/createdb/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
name: foldseek_createdb
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::foldseek=8.ef4e960
- bioconda::foldseek=9.427df8a
35 changes: 17 additions & 18 deletions modules/nf-core/foldseek/createdb/main.nf
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Expand Up @@ -4,8 +4,8 @@ process FOLDSEEK_CREATEDB {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/foldseek:8.ef4e960--pl5321hb365157_0':
'biocontainers/foldseek:8.ef4e960--pl5321hb365157_0' }"
'https://depot.galaxyproject.org/singularity/foldseek:9.427df8a--pl5321hb365157_0':
'biocontainers/foldseek:9.427df8a--pl5321hb365157_0' }"

input:
tuple val(meta), path(pdb)
Expand Down Expand Up @@ -39,22 +39,21 @@ process FOLDSEEK_CREATEDB {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
mkdir -p targetDB
touch ${prefix}
touch ${prefix}_ca
touch ${prefix}_ca.dbtype
touch ${prefix}_ca.index
touch ${prefix}_h
touch ${prefix}_h.dbtype
touch ${prefix}_h.index
touch ${prefix}_ss
touch ${prefix}_ss.dbtype
touch ${prefix}_ss.index
touch ${prefix}.dbtype
touch ${prefix}.index
touch ${prefix}.lookup
touch ${prefix}.source
mv ${prefix}* targetDB
mkdir -p ${prefix}
touch ${prefix}/${prefix}
touch ${prefix}/${prefix}_ca
touch ${prefix}/${prefix}_ca.dbtype
touch ${prefix}/${prefix}_ca.index
touch ${prefix}/${prefix}_h
touch ${prefix}/${prefix}_h.dbtype
touch ${prefix}/${prefix}_h.index
touch ${prefix}/${prefix}_ss
touch ${prefix}/${prefix}_ss.dbtype
touch ${prefix}/${prefix}_ss.index
touch ${prefix}/${prefix}.dbtype
touch ${prefix}/${prefix}.index
touch ${prefix}/${prefix}.lookup
touch ${prefix}/${prefix}.source

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/foldseek/createdb/meta.yml
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Expand Up @@ -13,7 +13,7 @@ tools:
documentation: "https://github.com/steineggerlab/foldseek"
tool_dev_url: "https://github.com/steineggerlab/foldseek"
doi: "10.1038/s41587-023-01773-0"
licence: "['GPL v3']"
licence: ["GPL v3"]
input:
- meta:
type: map
Expand Down
30 changes: 23 additions & 7 deletions modules/nf-core/foldseek/createdb/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,9 @@ nextflow_process {
tag "foldseek"
tag "foldseek/createdb"

test("Should build a protein structures database") {
test("proteomics - pdb") {

when {
params {
outdir = "$outputDir"
}
process {
"""
input[0] = [ [id:'test'], file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ]
Expand All @@ -23,12 +20,31 @@ nextflow_process {

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

}

test("proteomics - pdb - stub") {

options "-stub"

when {
process {
"""
input[0] = [ [id:'test'], file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ]
"""
}
}

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

}
}
134 changes: 112 additions & 22 deletions modules/nf-core/foldseek/createdb/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,30 +1,120 @@
{
"db": {
"proteomics - pdb": {
"content": [
[
[
{
"id": "test"
},
{
"0": [
[
"test:md5,5509f0851612be656f0659d62e290366",
"test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test.index:md5,e7eb45c3cbd57553ff8f024c7c83ed11",
"test.lookup:md5,bc6d0e967a6b30342597737ea862ae62",
"test.source:md5,42c68f3f5196a489d80b6d26ac8ac5f6",
"test_ca:md5,a5c5ffa9e813f7c35ed9a2737d4ef786",
"test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
"test_ca.index:md5,4020bfeefff484c9c973a895fa76c4bd",
"test_h:md5,6420b4e4730941b10e159971f826e74b",
"test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
"test_h.index:md5,e194f33e47acf6d687d572a45b784550",
"test_ss:md5,88d06580a2ee6a6a81a7821a423013a9",
"test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test_ss.index:md5,e7eb45c3cbd57553ff8f024c7c83ed11"
{
"id": "test"
},
[
"test:md5,5509f0851612be656f0659d62e290366",
"test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test.index:md5,e7eb45c3cbd57553ff8f024c7c83ed11",
"test.lookup:md5,3e653ea1ae44ba5404342b37c72f05f6",
"test.source:md5,1144e80754b5ba7bd85670e2be1c96db",
"test_ca:md5,a5c5ffa9e813f7c35ed9a2737d4ef786",
"test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
"test_ca.index:md5,4020bfeefff484c9c973a895fa76c4bd",
"test_h:md5,eb1f0b213589e93fa639d3ae91bcff2f",
"test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
"test_h.index:md5,11940a92d3235f31b8a487c59a1ff812",
"test_ss:md5,88d06580a2ee6a6a81a7821a423013a9",
"test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test_ss.index:md5,e7eb45c3cbd57553ff8f024c7c83ed11"
]
]
],
"1": [
"versions.yml:md5,02cfa3c3fbc560c23e27f604a55cb952"
],
"db": [
[
{
"id": "test"
},
[
"test:md5,5509f0851612be656f0659d62e290366",
"test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test.index:md5,e7eb45c3cbd57553ff8f024c7c83ed11",
"test.lookup:md5,3e653ea1ae44ba5404342b37c72f05f6",
"test.source:md5,1144e80754b5ba7bd85670e2be1c96db",
"test_ca:md5,a5c5ffa9e813f7c35ed9a2737d4ef786",
"test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
"test_ca.index:md5,4020bfeefff484c9c973a895fa76c4bd",
"test_h:md5,eb1f0b213589e93fa639d3ae91bcff2f",
"test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
"test_h.index:md5,11940a92d3235f31b8a487c59a1ff812",
"test_ss:md5,88d06580a2ee6a6a81a7821a423013a9",
"test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test_ss.index:md5,e7eb45c3cbd57553ff8f024c7c83ed11"
]
]
],
"versions": [
"versions.yml:md5,02cfa3c3fbc560c23e27f604a55cb952"
]
}
],
"timestamp": "2024-07-02T14:04:11.393697557"
},
"proteomics - pdb - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"test:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.index:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.source:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ca:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ca.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ca.index:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_h:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ss:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ss.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ss.index:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
"versions.yml:md5,02cfa3c3fbc560c23e27f604a55cb952"
],
"db": [
[
{
"id": "test"
},
[
"test:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.index:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
"test.source:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ca:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ca.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ca.index:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_h:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ss:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ss.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_ss.index:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,02cfa3c3fbc560c23e27f604a55cb952"
]
]
}
],
"timestamp": "2023-11-09T11:03:51.066468346"
"timestamp": "2024-07-02T14:04:15.995578638"
}
}
3 changes: 2 additions & 1 deletion modules/nf-core/foldseek/easysearch/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
name: foldseek_easysearch
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::foldseek=8.ef4e960
- bioconda::foldseek=9.427df8a
4 changes: 2 additions & 2 deletions modules/nf-core/foldseek/easysearch/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process FOLDSEEK_EASYSEARCH {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/foldseek:8.ef4e960--pl5321hb365157_0':
'biocontainers/foldseek:8.ef4e960--pl5321hb365157_0' }"
'https://depot.galaxyproject.org/singularity/foldseek:9.427df8a--pl5321hb365157_0':
'biocontainers/foldseek:9.427df8a--pl5321hb365157_0' }"

input:
tuple val(meta) , path(pdb)
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/foldseek/easysearch/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ tools:
documentation: "https://github.com/steineggerlab/foldseek"
tool_dev_url: "https://github.com/steineggerlab/foldseek"
doi: "10.1038/s41587-023-01773-0"
licence: "['GPL v3']"
licence: ["GPL v3"]
input:
- meta:
type: map
Expand Down
50 changes: 35 additions & 15 deletions modules/nf-core/foldseek/easysearch/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -6,25 +6,46 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "foldseek"
tag "foldseek/createdb"
tag "foldseek/easysearch"

test("Should search for protein structural hits against a protein structures database") {

setup {
run("FOLDSEEK_CREATEDB") {
script "../../createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_db' ], [ file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ] ]
"""
}
setup {
run("FOLDSEEK_CREATEDB") {
script "../../createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_db' ], [ file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ] ]
"""
}
}
}

test("proteomics - pdb") {

when {
params {
outdir = "$outputDir"
process {
"""
input[0] = [ [ id:'test_search' ], [ file(params.test_data['proteomics']['pdb']['tim8_pdb'], checkIfExists: true) ] ]
input[1] = FOLDSEEK_CREATEDB.out.db
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.aln.get(0).get(1)).readLines().contains("8tim_A\t1tim_A\t0.967\t247\t8\t0\t1\t247\t1\t247\t1.152E-43\t1523") },
{ assert process.out.versions }
)
}

}

test("proteomics - pdb -stub") {

options "-stub"

when {
process {
"""
input[0] = [ [ id:'test_search' ], [ file(params.test_data['proteomics']['pdb']['tim8_pdb'], checkIfExists: true) ] ]
Expand All @@ -35,9 +56,8 @@ nextflow_process {

then {
assertAll(
{ assert process.success },
{ assert path(process.out.aln.get(0).get(1)).readLines().contains("8tim.pdb_A\t1tim.pdb_A\t0.967\t247\t8\t0\t1\t247\t1\t247\t1.152E-43\t1523") },
{ assert process.out.versions }
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

Expand Down
31 changes: 31 additions & 0 deletions modules/nf-core/foldseek/easysearch/tests/main.nf.test.snap
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@@ -0,0 +1,31 @@
{
"proteomics - pdb -stub": {
"content": [
{
"0": [
[
{
"id": "test_search"
},
"test_search.m8:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,ddc75b2e08b63a7082ecad353073fd3b"
],
"aln": [
[
{
"id": "test_search"
},
"test_search.m8:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,ddc75b2e08b63a7082ecad353073fd3b"
]
}
],
"timestamp": "2024-07-02T13:55:57.915188646"
}
}
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