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Remove compressed flag from all mmseqs modules #7211

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Remove compressed flag from all mmseqs modules #7211

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b886a8b
Remove `compressed` flags from all mmmseqs modules
jasmezz Dec 12, 2024
2dc53e5
Update snapshots
SPPearce Dec 15, 2024
0ad5588
Merge branch 'master' into fix-mmseqs-compressed
SPPearce Dec 15, 2024
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3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/cluster/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,7 @@ process MMSEQS_CLUSTER {
${prefix}/${prefix} \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1
--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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6 changes: 3 additions & 3 deletions modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap
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Expand Up @@ -8,15 +8,15 @@
"test_output_cluster.index"
],
[
"test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089",
"test_output_cluster.index:md5,ca7e1f0967222b06d7e05e47bcbe1e50"
"test_output_cluster.dbtype:md5,b9d9c6dbc098c97ae446f612efd8eafd",
"test_output_cluster.index:md5,9848b52b6df827d80a04f7c71c50056b"
],
"versions.yml:md5,4acad55952c6d1fb41ad7f5a44468aed"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T10:44:45.713270981"
"timestamp": "2024-12-15T19:30:14.704271821"
}
}
3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/createdb/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,7 @@ process MMSEQS_CREATEDB {
createdb \\
${sequence_name} \\
${prefix}/${prefix} \\
$args \\
--compressed 1
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
28 changes: 14 additions & 14 deletions modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,14 +8,14 @@
"single_end": false
},
[
"test:md5,7c3c2c5926cf8fa82e66b9628f680256",
"test.dbtype:md5,c8ed20c23ba91f4577f84c940c86c7db",
"test.index:md5,5b2fd8abd0ad3fee24738af7082e6a6e",
"test:md5,a2cda8768736a7a317a09d61556194bd",
"test.dbtype:md5,4352d88a78aa39750bf70cd6f27bcaa5",
"test.index:md5,4ba298b011e2472ce9f6b99fe6b6e3d5",
"test.lookup:md5,32f88756dbcb6aaf7b239b0d61730f1b",
"test.source:md5,9ada5b3ea6e1a7e16c4418eb98ae8d9d",
"test_h:md5,8c29f5ed94d83d7115e9c8a883ce358d",
"test_h.dbtype:md5,8895d3d8e9322aedbf45249dfb3ddb0a",
"test_h.index:md5,87c7c8c6d16018ebfaa6f408391a5ae2"
"test_h:md5,21c399702a071bdeecce09f9d1df4531",
"test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
"test_h.index:md5,d767fb43b37c0a644c676b00f9f93477"
]
]
],
Expand All @@ -27,7 +27,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T10:35:27.322864475"
"timestamp": "2024-12-15T19:30:25.339409238"
},
"Should build an mmseqs db from a zipped amino acid sequence file": {
"content": [
Expand All @@ -37,14 +37,14 @@
"id": "test"
},
[
"test:md5,4b494965ed7ab67da8ca3f39523eb104",
"test.dbtype:md5,152afd7bf4dbe26f85032eee0269201a",
"test.index:md5,46f9d884e9a7f442fe1cd2ce339734e3",
"test:md5,1162504bc65aacf734abdcb0cdbe87de",
"test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
"test.index:md5,8cdcbc06c2b99fdb09f3d1735a76def9",
"test.lookup:md5,3e27cb93d9ee875ad42a6f32f5651bdc",
"test.source:md5,eaa64fc8a5f7ec1ee49b0dcbd1a72e9d",
"test_h:md5,6e798b81c70d191f78939c2dd6223a7f",
"test_h.dbtype:md5,8895d3d8e9322aedbf45249dfb3ddb0a",
"test_h.index:md5,d5ac49ff56df064b980fa0eb5da57673"
"test_h:md5,f258f8cc04f83c270a75e8b00a6d2d89",
"test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
"test_h.index:md5,844bf1950bcd37284fdc5d7117ee4241"
]
]
],
Expand All @@ -56,6 +56,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T10:35:33.418552595"
"timestamp": "2024-12-15T19:30:34.93361715"
}
}
3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/createindex/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,7 @@ process MMSEQS_CREATEINDEX {
\${DB_INPUT_PATH_NAME} \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1
--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/createtsv/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,7 @@ process MMSEQS_CREATETSV {
\$DB_RESULT_PATH_NAME \\
${prefix}.tsv \\
$args \\
--threads ${task.cpus} \\
--compressed 1
--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
1 change: 0 additions & 1 deletion modules/nf-core/mmseqs/databases/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ process MMSEQS_DATABASES {
${prefix}/database \\
tmp/ \\
--threads ${task.cpus} \\
--compressed 1 \\
${args}

cat <<-END_VERSIONS > versions.yml
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3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/easysearch/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,7 @@ process MMSEQS_EASYSEARCH {
${prefix}.tsv \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1
--threads ${task.cpus}


cat <<-END_VERSIONS > versions.yml
Expand Down
3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/linclust/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,7 @@ process MMSEQS_LINCLUST {
${prefix}/${prefix} \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1
--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,15 @@
"test_output_cluster.index"
],
[
"test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089",
"test_output_cluster.index:md5,38908275cdd5727ae0eb9be017f9ca13"
"test_output_cluster.dbtype:md5,b9d9c6dbc098c97ae446f612efd8eafd",
"test_output_cluster.index:md5,a0b78f31aee2c327d72f32919814baf1"
],
"versions.yml:md5,969cb26241f66ac758c104f9561860b1"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-05T10:43:26.020522437"
"timestamp": "2024-12-15T19:38:00.258247122"
}
}
4 changes: 1 addition & 3 deletions modules/nf-core/mmseqs/search/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,7 @@ process MMSEQS_SEARCH {
${prefix}/${prefix} \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1

--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
3 changes: 1 addition & 2 deletions modules/nf-core/mmseqs/taxonomy/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,7 @@ process MMSEQS_TAXONOMY {
${prefix}_taxonomy/${prefix} \\
tmp1 \\
$args \\
--threads ${task.cpus} \\
--compressed 1
--threads ${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
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