From dd5a4a815cb55ca6214e76c1b2e6df4847cdd0f3 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 9 Sep 2021 09:44:59 +0200
Subject: [PATCH 1/3] Replace tokenize to basename

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

diff --git a/main.nf b/main.nf
index a9b87a6d0..4b42bf496 100644
--- a/main.nf
+++ b/main.nf
@@ -2977,7 +2977,7 @@ process kraken {
   tuple prefix, path("*.kraken2_report") into ch_kraken_report, ch_kraken_for_multiqc
 
   script:
-  prefix = fastq.toString().tokenize('.')[0]
+  prefix = fastq.basename
   out = prefix+".kraken.out"
   kreport = prefix+".kraken2_report"
   kreport_old = prefix+".kreport"

From d3a4258923649b30c202f768c4c56a4a941b81d8 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 9 Sep 2021 09:48:10 +0200
Subject: [PATCH 2/3] Update CHANGELOG.md

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 422077b66..2c7ed9289 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Updated workflow diagrams to reflect latest functionality
 - [#787](https://github.com/nf-core/eager/issues/787) Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander)
 - Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
+- [#790](https://github.com/nf-core/eager/issues/790) Fixed kraken2 report file-name collision when sample names have `.` in them
 
 ### `Dependencies`
 

From 82cc021202ef31f5f83fbbc1f4044a0c07375193 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 9 Sep 2021 09:55:51 +0200
Subject: [PATCH 3/3] Remove NF warn message and fix baseName

---
 main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 4b42bf496..a3a42a489 100644
--- a/main.nf
+++ b/main.nf
@@ -237,12 +237,12 @@ if ( !params.clip_adapters_list ) {
     Channel
       .fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
       .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
-      .into {ch_adapterlist}
+      .set {ch_adapterlist}
 } else {
     Channel
       .fromPath("${params.clip_adapters_list}", checkIfExists: true)
       .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
-      .into {ch_adapterlist}
+      .set {ch_adapterlist}
 }
 
 
@@ -2977,7 +2977,7 @@ process kraken {
   tuple prefix, path("*.kraken2_report") into ch_kraken_report, ch_kraken_for_multiqc
 
   script:
-  prefix = fastq.basename
+  prefix = fastq.baseName
   out = prefix+".kraken.out"
   kreport = prefix+".kraken2_report"
   kreport_old = prefix+".kreport"