Merge pull request #54 from skrakau/fix_db_name

Adjusted handling of compressed tar archive containing kraken2 database
nf-core · Jun 23, 2020 · 748c779 · 748c779
2 parents 22464a2 + 7ec13a4
commit 748c779
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Fix missing MultiQC when `--skip_quast` or `--skip_busco` was specified
 - Fix missing channels when `--keep_phix` is specified
 - Added missing parameters to summary
+- Updated links to minikraken db
+- Fixed kraken2 dp preparation: allow different names for compressed archive file and contained folder as for some minikraken dbs
 
 ### `Deprecated`
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -228,7 +228,7 @@ Database for taxonomic binning with centrifuge (default: none). E.g. "<ftp://ftp
 
 ### `--kraken2_db`
 
-Database for taxonomic binning with kraken2 (default: none). E.g. "<ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz>"
+Database for taxonomic binning with kraken2 (default: none). E.g. "<ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz>"
 
 ### `--cat_db`
 

diff --git a/main.nf b/main.nf
@@ -70,7 +70,7 @@ def helpMessage() {
 
     Taxonomy:
       --centrifuge_db [file]                Database for taxonomic binning with centrifuge (default: none). E.g. "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz"
-      --kraken2_db [file]                   Database for taxonomic binning with kraken2 (default: none). E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz"
+      --kraken2_db [file]                   Database for taxonomic binning with kraken2 (default: none). E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz"
       --skip_krona [bool]                   Skip creating a krona plot for taxonomic binning
       --cat_db [file]                       Database for taxonomic classification of metagenome assembled genomes (default: none). E.g. "tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190108.tar.gz"
                                             The zipped file needs to contain a folder named "*taxonomy*" and "*CAT_database*" that hold the respective files.
@@ -777,7 +777,7 @@ process kraken2_db_preparation {
     file(db) from file_kraken2_db
 
     output:
-    set val("${db.baseName}"), file("${db.baseName}/*.k2d") into kraken2_database
+    set val("${db.baseName}"), file("*/*.k2d") into kraken2_database
 
     script:
     """