Merge pull request #673 from maxibor/dev

Fix kraken db loading fromPath

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#631](https://github.com/nf-core/eager/issues/631): - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
 - Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
 - Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data.  `
+- [#673](https://github.com/nf-core/eager/pull/673): Fix Kraken database loading when loading from directory instead of compressed file.
 
 ### `Dependencies`
 

main.nf

@@ -3108,14 +3108,16 @@ if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && p
     path(dbname) into ch_krakendb
 
     script:
-    dbname = params.database.tokenize("/")[-1].tokenize(".")[0]
+    dbname = ckdb.toString() - '.tar.gz'
     """
     tar xvzf $ckdb
+    mkdir -p $dbname
+    mv *.k2d $dbname || echo "nothing to do"
     """
   }
 
 } else if (! params.database.endsWith(".tar.gz") && params.run_metagenomic_screening && params.metagenomic_tool == 'kraken') {
-    ch_krakendb = path(params.database)
+    ch_krakendb = Channel.fromPath(params.database).first()
 } else {
     ch_krakendb = Channel.empty()
 }