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Bump GTDBTk to v2.4.0 #664

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merged 4 commits into from
Sep 10, 2024
Merged

Bump GTDBTk to v2.4.0 #664

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df02613
Update GTDBTk to v2.4.0
dialvarezs Sep 8, 2024
e4fa8a9
Changelog
dialvarezs Sep 8, 2024
5580375
Prettier
dialvarezs Sep 8, 2024
080eac6
Bump GTDB release version, better changelog
jfy133 Sep 9, 2024
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,10 +9,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)

### `Fixed`

### `Dependencies`

| Tool | Previous version | New version |
| ------ | ---------------- | ----------- |
| GTDBTk | 2.3.2 | 2.4.0 |

### `Deprecated`

## 3.0.3 [2024-08-27]
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10 changes: 5 additions & 5 deletions bin/summary_gtdbtk.py
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Expand Up @@ -76,11 +76,11 @@ def main(args=None):
columns = [
"user_genome",
"classification",
"fastani_reference",
"fastani_reference_radius",
"fastani_taxonomy",
"fastani_ani",
"fastani_af",
"closest_genome_reference",
"closest_genome_reference_radius",
"closest_genome_taxonomy",
"closest_genome_ani",
"closest_genome_af",
"closest_placement_reference",
"closest_placement_radius",
"closest_placement_taxonomy",
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2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -22,7 +22,7 @@ params {
//centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
// gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz"
// gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" ## This should be updated to release 220, once we get GTDB-Tk working again
skip_gtdbtk = true

// TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -124,7 +124,7 @@
},
"gtdbtk/classifywf": {
"branch": "master",
"git_sha": "0735b6d2b509cbb5cf71d15fda819cd7392722fe",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"gunc/downloaddb": {
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4 changes: 1 addition & 3 deletions modules/nf-core/gtdbtk/classifywf/environment.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/gtdbtk/classifywf/main.nf
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -87,7 +87,7 @@ params {
cat_official_taxonomy = false
save_cat_db = false
skip_gtdbtk = false
gtdb_db = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz"
gtdb_db = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
gtdb_mash = null
gtdbtk_min_completeness = 50.0
gtdbtk_max_contamination = 10.0
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -537,7 +537,7 @@
"gtdb_db": {
"type": "string",
"description": "Specify the location of a GTDBTK database. Can be either an uncompressed directory or a `.tar.gz` archive. If not specified will be downloaded for you when GTDBTK or binning QC is not skipped.",
"default": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz"
"default": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
},
"gtdb_mash": {
"type": "string",
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