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dialvarezsdialvarezs
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Update mmseqs modules to v18 (#9331)
* Update all mmseqs modules * Update snapshots * Update more snapshots * Update metaeuk snapshot
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+255
-239
lines changed

40 files changed

+255
-239
lines changed

‎modules/nf-core/metaeuk/easypredict/tests/main.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ nextflow_process {
4141

4242
process {
4343
"""
44-
input[0] = 'UniProtKB/Swiss-Prot'
44+
input[0] = 'Kalamari'
4545
"""
4646
}
4747
}

‎modules/nf-core/metaeuk/easypredict/tests/main.nf.test.snap‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -174,31 +174,31 @@
174174
{
175175
"id": "test"
176176
},
177-
"test.fas:md5,3834a7d4dc4f7da755afc00b73589a1b"
177+
"test.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
178178
]
179179
],
180180
"1": [
181181
[
182182
{
183183
"id": "test"
184184
},
185-
"test.codon.fas:md5,21e47f601e73834f96a61f5150535716"
185+
"test.codon.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
186186
]
187187
],
188188
"2": [
189189
[
190190
{
191191
"id": "test"
192192
},
193-
"test.headersMap.tsv:md5,518ed985e5dad185ba2e8228c540c059"
193+
"test.headersMap.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
194194
]
195195
],
196196
"3": [
197197
[
198198
{
199199
"id": "test"
200200
},
201-
"test.gff:md5,0d1e318931bb2b441fbc035137b7fc49"
201+
"test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
202202
]
203203
],
204204
"4": [
@@ -209,31 +209,31 @@
209209
{
210210
"id": "test"
211211
},
212-
"test.codon.fas:md5,21e47f601e73834f96a61f5150535716"
212+
"test.codon.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
213213
]
214214
],
215215
"faa": [
216216
[
217217
{
218218
"id": "test"
219219
},
220-
"test.fas:md5,3834a7d4dc4f7da755afc00b73589a1b"
220+
"test.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
221221
]
222222
],
223223
"gff": [
224224
[
225225
{
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"id": "test"
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},
228-
"test.gff:md5,0d1e318931bb2b441fbc035137b7fc49"
228+
"test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
229229
]
230230
],
231231
"tsv": [
232232
[
233233
{
234234
"id": "test"
235235
},
236-
"test.headersMap.tsv:md5,518ed985e5dad185ba2e8228c540c059"
236+
"test.headersMap.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
237237
]
238238
],
239239
"versions": [
@@ -243,8 +243,8 @@
243243
],
244244
"meta": {
245245
"nf-test": "0.9.2",
246-
"nextflow": "25.04.6"
246+
"nextflow": "25.10.0"
247247
},
248-
"timestamp": "2025-09-25T08:18:53.256041749"
248+
"timestamp": "2025-11-01T17:50:24.868686992"
249249
}
250250
}

‎modules/nf-core/mmseqs/cluster/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::mmseqs2=17.b804f
7+
- bioconda::mmseqs2=18.8cc5c

‎modules/nf-core/mmseqs/cluster/main.nf‎

Lines changed: 11 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,18 @@
11
process MMSEQS_CLUSTER {
2-
tag "$meta.id"
2+
tag "${meta.id}"
33
label 'process_high'
44

55
conda "${moduleDir}/environment.yml"
6-
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
8-
'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
6+
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
7+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
8+
: 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
99

1010
input:
1111
tuple val(meta), path(db_input)
1212

1313
output:
1414
tuple val(meta), path("${prefix}/"), emit: db_cluster
15-
path "versions.yml" , emit: versions
15+
path "versions.yml", emit: versions
1616

1717
when:
1818
task.ext.when == null || task.ext.when
@@ -21,19 +21,21 @@ process MMSEQS_CLUSTER {
2121
def args = task.ext.args ?: ''
2222
def args2 = task.ext.args2 ?: "*.dbtype"
2323
prefix = task.ext.prefix ?: "${meta.id}"
24-
if ("$db_input" == "${prefix}") error "Input and output names of databases are the same, set prefix in module configuration to disambiguate!"
24+
if ("${db_input}" == "${prefix}") {
25+
error("Input and output names of databases are the same, set prefix in module configuration to disambiguate!")
26+
}
2527

2628
"""
2729
mkdir -p ${prefix}
2830
# Extract files with specified args based suffix | remove suffix | isolate longest common substring of files
29-
DB_INPUT_PATH_NAME=\$(find -L "$db_input/" -maxdepth 1 -name "$args2" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
31+
DB_INPUT_PATH_NAME=\$(find -L "${db_input}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
3032
3133
mmseqs \\
3234
cluster \\
3335
\$DB_INPUT_PATH_NAME \\
3436
${prefix}/${prefix} \\
3537
tmp1 \\
36-
$args \\
38+
${args} \\
3739
--threads ${task.cpus}
3840
3941
cat <<-END_VERSIONS > versions.yml
@@ -46,6 +48,7 @@ process MMSEQS_CLUSTER {
4648
def args = task.ext.args ?: ''
4749
prefix = task.ext.prefix ?: "${meta.id}"
4850
"""
51+
echo ${args}
4952
mkdir -p ${prefix}
5053
5154
touch ${prefix}/${prefix}.{0..9}

‎modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -11,12 +11,12 @@
1111
"test_output_cluster.dbtype:md5,b9d9c6dbc098c97ae446f612efd8eafd",
1212
"test_output_cluster.index:md5,9848b52b6df827d80a04f7c71c50056b"
1313
],
14-
"versions.yml:md5,8cd8fdc3e9d128b0a4dc634b8748c213"
14+
"versions.yml:md5,b53987961652676f677105ea360a633f"
1515
],
1616
"meta": {
1717
"nf-test": "0.9.2",
18-
"nextflow": "24.10.3"
18+
"nextflow": "25.10.0"
1919
},
20-
"timestamp": "2025-01-20T14:07:52.454357"
20+
"timestamp": "2025-11-01T16:18:22.334709172"
2121
}
2222
}

‎modules/nf-core/mmseqs/createdb/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::mmseqs2=17.b804f
7+
- bioconda::mmseqs2=18.8cc5c

‎modules/nf-core/mmseqs/createdb/main.nf‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,18 @@
11
process MMSEQS_CREATEDB {
2-
tag "$meta.id"
2+
tag "${meta.id}"
33
label 'process_low'
44

55
conda "${moduleDir}/environment.yml"
6-
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
8-
'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
6+
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
7+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
8+
: 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
99

1010
input:
1111
tuple val(meta), path(sequence)
1212

1313
output:
1414
tuple val(meta), path("${prefix}/"), emit: db
15-
path "versions.yml" , emit: versions
15+
path "versions.yml", emit: versions
1616

1717
when:
1818
task.ext.when == null || task.ext.when
@@ -33,7 +33,7 @@ process MMSEQS_CREATEDB {
3333
createdb \\
3434
${sequence_name} \\
3535
${prefix}/${prefix} \\
36-
$args
36+
${args}
3737
3838
cat <<-END_VERSIONS > versions.yml
3939
"${task.process}":
@@ -45,6 +45,7 @@ process MMSEQS_CREATEDB {
4545
def args = task.ext.args ?: ''
4646
prefix = task.ext.prefix ?: "${meta.id}"
4747
"""
48+
echo ${args}
4849
mkdir -p ${prefix}
4950
5051
touch ${prefix}/${prefix}

‎modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -20,14 +20,14 @@
2020
]
2121
],
2222
[
23-
"versions.yml:md5,c62b08152082097334109fe08ec6333a"
23+
"versions.yml:md5,02a6806d10988baae0ab644d671f113c"
2424
]
2525
],
2626
"meta": {
2727
"nf-test": "0.9.2",
28-
"nextflow": "24.10.3"
28+
"nextflow": "25.10.0"
2929
},
30-
"timestamp": "2025-01-20T14:11:57.883871"
30+
"timestamp": "2025-11-01T16:18:26.983758708"
3131
},
3232
"Should build an mmseqs db from a zipped amino acid sequence file": {
3333
"content": [
@@ -49,13 +49,13 @@
4949
]
5050
],
5151
[
52-
"versions.yml:md5,c62b08152082097334109fe08ec6333a"
52+
"versions.yml:md5,02a6806d10988baae0ab644d671f113c"
5353
]
5454
],
5555
"meta": {
5656
"nf-test": "0.9.2",
57-
"nextflow": "24.10.3"
57+
"nextflow": "25.10.0"
5858
},
59-
"timestamp": "2025-01-20T14:12:10.986433"
59+
"timestamp": "2025-11-01T16:18:31.492266142"
6060
}
6161
}

‎modules/nf-core/mmseqs/createindex/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::mmseqs2=17.b804f
7+
- bioconda::mmseqs2=18.8cc5c

‎modules/nf-core/mmseqs/createindex/main.nf‎

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,8 @@ process MMSEQS_CREATEINDEX {
55

66
conda "${moduleDir}/environment.yml"
77
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
8-
? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1'
9-
: 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}"
8+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
9+
: 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
1010

1111
input:
1212
tuple val(meta), path(db)
@@ -21,8 +21,6 @@ process MMSEQS_CREATEINDEX {
2121
script:
2222
def args = task.ext.args ?: ''
2323
def args2 = task.ext.args2 ?: "*.dbtype"
24-
def prefix = task.ext.prefix ?: "${meta.id}"
25-
2624
"""
2725
DB_INPUT_PATH_NAME=\$(find -L "${db}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
2826
@@ -45,7 +43,7 @@ process MMSEQS_CREATEINDEX {
4543
"""
4644
DB_INPUT_PATH_NAME=\$(find -L "${db}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
4745
48-
touch "\${DB_PATH_NAME}.idx"
46+
touch "\${DB_INPUT_PATH_NAME}.idx"
4947
5048
cat <<-END_VERSIONS > versions.yml
5149
"${task.process}":

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