Updated PFR's Kraken 2 database to k2_pluspfp_20240904

Plant-Food-Research-Open · Nov 4, 2024 · af5c449 · af5c449
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 10. Updated the tube map along with the tool list [#166](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/166)
 11. Added Orthofinder [#167](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/167)
 12. Changed order of tool options in the `nextflow.config` file
+13. Updated PFR's Kraken 2 database to `k2_pluspfp_20240904` [#170](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/170)
 
 ### `Fixed`
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -65,7 +65,7 @@ BUSCO lineage databases are downloaded and updated by the BUSCO tool itself. A p
 
 ### Kraken 2
 
-Path to Kraken 2 database is provided by the `kraken2_db_path` parameter. This can be a URL to a public `.tar.gz` file such as `https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240112.tar.gz`. The pipeline can download and extract the database. This is not the recommended practice owing to the size of the database. Rather, the database should be downloaded, extracted and stored in a read-only location. The path to that location can be provided by the `kraken2_db_path` parameter such as `/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314`.
+Path to Kraken 2 database is provided by the `kraken2_db_path` parameter. This can be a URL to a public `.tar.gz` file such as `https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240112.tar.gz`. The pipeline can download and extract the database. This is not the recommended practice owing to the size of the database. Rather, the database should be downloaded, extracted and stored in a read-only location. The path to that location can be provided by the `kraken2_db_path` parameter such as `/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904`.
 
 ## Other parameters
 

diff --git a/pfr/params.json b/pfr/params.json
@@ -21,7 +21,7 @@
     "busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc",
     "lai_skip": false,
     "kraken2_skip": false,
-    "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314",
+    "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904",
     "hic": null,
     "hic_skip_fastp": false,
     "hic_skip_fastqc": false,

diff --git a/pfr_assemblyqc b/pfr_assemblyqc
@@ -40,7 +40,7 @@ if [ $full_test_flag -eq 1 ]; then
         --ncbi_fcs_gx_skip false \
         --ncbi_fcs_gx_db_path "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24" \
         --kraken2_skip false \
-        --kraken2_db_path "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314" \
+        --kraken2_db_path "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904" \
         -resume \
         --outdir results
 else