From 0468dfa3e83345fc2bd304392ca7dfd416347b0a Mon Sep 17 00:00:00 2001
From: Maxime Borry <borry@mpi-sdag1>
Date: Mon, 1 Feb 2021 15:33:31 +0100
Subject: [PATCH 1/6] fix kraken db loading fromPath

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 88ebe9e4d..9b1082a2d 100644
--- a/main.nf
+++ b/main.nf
@@ -3115,7 +3115,7 @@ if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && p
   }
 
 } 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)
 } else {
     ch_krakendb = Channel.empty()
 }

From 1fd116d1e6306122d7f681f268fd998b0f82d7bd Mon Sep 17 00:00:00 2001
From: Maxime Borry <borry@mpi-sdag1>
Date: Mon, 1 Feb 2021 15:37:39 +0100
Subject: [PATCH 2/6] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a77fd4f28..4b4778ee4 100644
--- a/CHANGELOG.md
+++ b/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`
 

From f8fa322bd3e9e2f8a387c4f300a5c841d489088c Mon Sep 17 00:00:00 2001
From: Maxime Borry <borry@mpi-sdag1>
Date: Mon, 1 Feb 2021 15:43:11 +0100
Subject: [PATCH 3/6] change basenaming of database

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 70a59069c..71718973d 100644
--- a/main.nf
+++ b/main.nf
@@ -3108,7 +3108,7 @@ 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 = params.database.toString() - '.tar.gz'
     """
     tar xvzf $ckdb
     """

From 67247702c51959ee03d5bb87227de1fb0f129e3c Mon Sep 17 00:00:00 2001
From: Maxime Borry <borry@mpi-sdag1>
Date: Mon, 1 Feb 2021 16:24:22 +0100
Subject: [PATCH 4/6] renaming archive files in decomp kraken

---
 main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 71718973d..65a87317f 100644
--- a/main.nf
+++ b/main.nf
@@ -3108,9 +3108,11 @@ if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && p
     path(dbname) into ch_krakendb
     
     script:
-    dbname = params.database.toString() - '.tar.gz'
+    dbname = ckdb.toString() - '.tar.gz'
     """
     tar xvzf $ckdb
+    mkdir -p $dbname
+    mv *.k2d $dbname
     """
   }
 

From fea32497737baef5e73c211bfcc3836ca08b5537 Mon Sep 17 00:00:00 2001
From: Maxime Borry <borry@mpi-sdag1>
Date: Tue, 2 Feb 2021 12:05:01 +0100
Subject: [PATCH 5/6] handle case when files are already in $dbdir

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 65a87317f..994390acb 100644
--- a/main.nf
+++ b/main.nf
@@ -3112,7 +3112,7 @@ if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && p
     """
     tar xvzf $ckdb
     mkdir -p $dbname
-    mv *.k2d $dbname
+    mv *.k2d $dbname || echo "nothing to do"
     """
   }
 

From d89b4cccb7297de739f37ee5b902f7e9897056fe Mon Sep 17 00:00:00 2001
From: Maxime Borry <borry@mpi-sdag1>
Date: Wed, 3 Feb 2021 15:13:43 +0100
Subject: [PATCH 6/6] transforms to value channel with .first()

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 994390acb..727c1c2fb 100644
--- a/main.nf
+++ b/main.nf
@@ -3117,7 +3117,7 @@ if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && p
   }
 
 } else if (! params.database.endsWith(".tar.gz") && params.run_metagenomic_screening && params.metagenomic_tool == 'kraken') {
-    ch_krakendb = Channel.fromPath(params.database)
+    ch_krakendb = Channel.fromPath(params.database).first()
 } else {
     ch_krakendb = Channel.empty()
 }