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Merge pull request #431 from nf-core/update-modules
Update several modules
2 parents 21f7969 + 6012d16 commit bda8f43

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‎CHANGELOG.md‎

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@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#427](https://github.com/nf-core/funcscan/pull/427) AMPcombi now can use multiple other databases for classifications. (by @darcy220606)
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- [#429](https://github.com/nf-core/funcscan/pull/429) Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz)
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- [#433](https://github.com/nf-core/funcscan/pull/433) Updated to nf-core template 3.1.1. (by @jfy133)
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- [#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)
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### `Fixed`
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@@ -21,11 +22,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Dependencies`
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| Tool | Previous version | New version |
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| -------- | ---------------- | ----------- |
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| AMPcombi | 0.2.2 | 2.0.1 |
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| Macrel | 1.2.0 | 1.4.0 |
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| MultiQC | 1.24.0 | 1.25.1 |
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| Tool | Previous version | New version |
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| --------- | ---------------- | ----------- |
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| AMPcombi | 0.2.2 | 2.0.1 |
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| Macrel | 1.2.0 | 1.4.0 |
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| MMseqs2 | 15.6f452 | 17.b804f |
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| MultiQC | 1.24.0 | 1.26 |
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| Pyrodigal | 3.3.0 | 3.6.3 |
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| seqkit | 2.8.1 | 2.9.0 |
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### `Deprecated`
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| GECCO | 0.9.8 | 0.9.10 |
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| hAMRonization | 1.1.1 | 1.1.4 |
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| HMMER | 3.3.2 | 3.4 |
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| MMSeqs | NA | 2:15.6f452 |
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| MMseqs2 | NA | 15.6f452 |
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| MultiQC | 1.15 | 1.24 |
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| Pyrodigal | 2.1.0 | 3.3.0 |
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| RGI | 5.2.1 | 6.0.3 |

‎conf/base.config‎

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@@ -156,6 +156,7 @@ process {
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withName: ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
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memory = { 4.GB * task.attempt }
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cpus = 1
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time = { 2.h * task.attempt }
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}
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withName: DEEPBGC_DOWNLOAD {

‎conf/modules.config‎

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@@ -41,7 +41,8 @@ process {
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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]
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ext.args = [
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params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files"
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params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files",
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"--compressed ${params.taxa_classification_mmseqs_compressed}"
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].join(' ').trim()
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}
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enabled: params.save_db,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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]
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ext.args = [
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"--compressed ${params.taxa_classification_mmseqs_compressed}"
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].join(' ').trim()
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}
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withName: MMSEQS_TAXONOMY {
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"--orf-filter-s ${params.taxa_classification_mmseqs_taxonomy_orffilters}",
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"--lca-mode ${params.taxa_classification_mmseqs_taxonomy_lcamode}",
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"--vote-mode ${params.taxa_classification_mmseqs_taxonomy_votemode}",
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"--compressed ${params.taxa_classification_mmseqs_compressed}"
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].join(' ').trim()
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}
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pattern: "*.tsv",
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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]
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ext.args = [
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"--compressed ${params.taxa_classification_mmseqs_compressed}"
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].join(' ').trim()
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}
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withName: SEQKIT_SEQ {

‎modules.json‎

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},
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"ampcombi2/parsetables": {
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"branch": "master",
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"git_sha": "993865fe60cb1569155fbbbe0cee113e1127abaf",
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"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
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"installed_by": ["modules"]
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},
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"ampir": {
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},
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"amplify/predict": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
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"installed_by": ["modules"]
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},
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"amrfinderplus/run": {
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},
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"bakta/bakta": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
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"installed_by": ["modules"]
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},
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"bakta/baktadbdownload": {
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},
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"deepbgc/download": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
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"installed_by": ["modules"]
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},
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"deepbgc/pipeline": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
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"installed_by": ["modules"]
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},
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"fargene": {
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
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"installed_by": ["modules"]
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},
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"hamronization/abricate": {
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},
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"mmseqs/createdb": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
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"installed_by": ["modules"]
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},
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"mmseqs/createtsv": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
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"installed_by": ["modules"]
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},
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"mmseqs/databases": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
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"installed_by": ["modules"]
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},
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"mmseqs/taxonomy": {
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"branch": "master",
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"git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
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"git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
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"git_sha": "f80914f78fb7fa1c00b14cfeb29575ee12240d9c",
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"installed_by": ["modules"]
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},
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"prodigal": {
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},
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"prokka": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "bcfb2f7efd4444ab442ffc8a248afbd62bca5ae7",
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"installed_by": ["modules"]
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},
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"pyrodigal": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "938e803109104e30773f76a7142442722498fef1",
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"installed_by": ["modules"]
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},
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"rgi/cardannotation": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
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"installed_by": ["modules"]
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},
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"rgi/main": {
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},
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"seqkit/seq": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "60645c2b45e56579de0a0c89416805cae44c1f46",
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"installed_by": ["modules"]
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},
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"tabix/bgzip": {
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},
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"untar": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/untar/untar.diff"
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}

‎modules/nf-core/ampcombi2/parsetables/meta.yml‎

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‎modules/nf-core/ampcombi2/parsetables/tests/tags.yml‎

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‎modules/nf-core/amplify/predict/tests/main.nf.test‎

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‎modules/nf-core/amplify/predict/tests/main.nf.test.snap‎

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‎modules/nf-core/bakta/bakta/meta.yml‎

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‎modules/nf-core/deepbgc/download/main.nf‎

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