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16 changes: 10 additions & 6 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#427](https://github.com/nf-core/funcscan/pull/427) AMPcombi now can use multiple other databases for classifications. (by @darcy220606)
- [#429](https://github.com/nf-core/funcscan/pull/429) Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz)
- [#433](https://github.com/nf-core/funcscan/pull/433) Updated to nf-core template 3.1.1. (by @jfy133)
- [#431](https://github.com/nf-core/funcscan/pull/431) Updated AMPcombi, Macrel, all MMseqs2 modules, MultiQC, Pyrodigal, and seqkit, added `--taxa_classification_mmseqs_compressed` parameter. (by @jasmezz)

### `Fixed`

Expand All @@ -21,11 +22,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Dependencies`

| Tool | Previous version | New version |
| -------- | ---------------- | ----------- |
| AMPcombi | 0.2.2 | 2.0.1 |
| Macrel | 1.2.0 | 1.4.0 |
| MultiQC | 1.24.0 | 1.25.1 |
| Tool | Previous version | New version |
| --------- | ---------------- | ----------- |
| AMPcombi | 0.2.2 | 2.0.1 |
| Macrel | 1.2.0 | 1.4.0 |
| MMseqs2 | 15.6f452 | 17.b804f |
| MultiQC | 1.24.0 | 1.26 |
| Pyrodigal | 3.3.0 | 3.6.3 |
| seqkit | 2.8.1 | 2.9.0 |

### `Deprecated`

Expand Down Expand Up @@ -105,7 +109,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| GECCO | 0.9.8 | 0.9.10 |
| hAMRonization | 1.1.1 | 1.1.4 |
| HMMER | 3.3.2 | 3.4 |
| MMSeqs | NA | 2:15.6f452 |
| MMseqs2 | NA | 15.6f452 |
| MultiQC | 1.15 | 1.24 |
| Pyrodigal | 2.1.0 | 3.3.0 |
| RGI | 5.2.1 | 6.0.3 |
Expand Down
1 change: 1 addition & 0 deletions conf/base.config
Original file line number Diff line number Diff line change
Expand Up @@ -156,6 +156,7 @@ process {
withName: ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
memory = { 4.GB * task.attempt }
cpus = 1
time = { 2.h * task.attempt }
}

withName: DEEPBGC_DOWNLOAD {
Expand Down
10 changes: 9 additions & 1 deletion conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,8 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
ext.args = [
params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files"
params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files",
"--compressed ${params.taxa_classification_mmseqs_compressed}"
].join(' ').trim()
}

Expand All @@ -52,6 +53,9 @@ process {
enabled: params.save_db,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
ext.args = [
"--compressed ${params.taxa_classification_mmseqs_compressed}"
].join(' ').trim()
}

withName: MMSEQS_TAXONOMY {
Expand All @@ -70,6 +74,7 @@ process {
"--orf-filter-s ${params.taxa_classification_mmseqs_taxonomy_orffilters}",
"--lca-mode ${params.taxa_classification_mmseqs_taxonomy_lcamode}",
"--vote-mode ${params.taxa_classification_mmseqs_taxonomy_votemode}",
"--compressed ${params.taxa_classification_mmseqs_compressed}"
].join(' ').trim()
}

Expand All @@ -81,6 +86,9 @@ process {
pattern: "*.tsv",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
ext.args = [
"--compressed ${params.taxa_classification_mmseqs_compressed}"
].join(' ').trim()
}

withName: SEQKIT_SEQ {
Expand Down
32 changes: 16 additions & 16 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
},
"ampcombi2/parsetables": {
"branch": "master",
"git_sha": "993865fe60cb1569155fbbbe0cee113e1127abaf",
"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
"installed_by": ["modules"]
},
"ampir": {
Expand All @@ -32,7 +32,7 @@
},
"amplify/predict": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
"installed_by": ["modules"]
},
"amrfinderplus/run": {
Expand Down Expand Up @@ -62,7 +62,7 @@
},
"bakta/bakta": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
"installed_by": ["modules"]
},
"bakta/baktadbdownload": {
Expand All @@ -82,12 +82,12 @@
},
"deepbgc/download": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
"installed_by": ["modules"]
},
"deepbgc/pipeline": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
"installed_by": ["modules"]
},
"fargene": {
Expand All @@ -102,7 +102,7 @@
},
"gunzip": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
"installed_by": ["modules"]
},
"hamronization/abricate": {
Expand Down Expand Up @@ -147,27 +147,27 @@
},
"mmseqs/createdb": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
"installed_by": ["modules"]
},
"mmseqs/createtsv": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
"installed_by": ["modules"]
},
"mmseqs/databases": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
"installed_by": ["modules"]
},
"mmseqs/taxonomy": {
"branch": "master",
"git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"git_sha": "f80914f78fb7fa1c00b14cfeb29575ee12240d9c",
"installed_by": ["modules"]
},
"prodigal": {
Expand All @@ -177,17 +177,17 @@
},
"prokka": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "bcfb2f7efd4444ab442ffc8a248afbd62bca5ae7",
"installed_by": ["modules"]
},
"pyrodigal": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "938e803109104e30773f76a7142442722498fef1",
"installed_by": ["modules"]
},
"rgi/cardannotation": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
"installed_by": ["modules"]
},
"rgi/main": {
Expand All @@ -197,7 +197,7 @@
},
"seqkit/seq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "60645c2b45e56579de0a0c89416805cae44c1f46",
"installed_by": ["modules"]
},
"tabix/bgzip": {
Expand All @@ -207,7 +207,7 @@
},
"untar": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
"installed_by": ["modules"],
"patch": "modules/nf-core/untar/untar.diff"
}
Expand Down
1 change: 0 additions & 1 deletion modules/nf-core/ampcombi2/parsetables/meta.yml

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2 changes: 2 additions & 0 deletions modules/nf-core/ampcombi2/parsetables/tests/tags.yml

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6 changes: 3 additions & 3 deletions modules/nf-core/amplify/predict/tests/main.nf.test

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8 changes: 4 additions & 4 deletions modules/nf-core/amplify/predict/tests/main.nf.test.snap

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4 changes: 2 additions & 2 deletions modules/nf-core/bakta/bakta/meta.yml

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20 changes: 15 additions & 5 deletions modules/nf-core/deepbgc/download/main.nf

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23 changes: 19 additions & 4 deletions modules/nf-core/deepbgc/download/tests/main.nf.test

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