From c1ff201518995463ec6624cc9eec6b287d1eeb0d Mon Sep 17 00:00:00 2001
From: Maxime Garcia <maxime.garcia@scilifelab.se>
Date: Fri, 12 Feb 2021 13:24:10 +0100
Subject: [PATCH] Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/bwamem2/index/main.nf  | 4 ++--
 software/bwamem2/index/meta.yml | 3 +--
 software/bwamem2/mem/meta.yml   | 5 ++---
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/software/bwamem2/index/main.nf b/software/bwamem2/index/main.nf
index e3b51a2b..36e4d4cd 100644
--- a/software/bwamem2/index/main.nf
+++ b/software/bwamem2/index/main.nf
@@ -22,14 +22,14 @@ process BWAMEM2_INDEX {
     path fasta
 
     output:
-    path "bwa"          , emit: index
+    path "bwamem2"          , emit: index
     path "*.version.txt", emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
     mkdir bwa
-    bwa-mem2 index $ioptions.args $fasta -p bwa/${fasta.baseName}
+    bwa-mem2 index $ioptions.args $fasta -p bwamem2/${fasta.baseName}
     echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
     """
 }
diff --git a/software/bwamem2/index/meta.yml b/software/bwamem2/index/meta.yml
index 3c7ba8c0..70780902 100644
--- a/software/bwamem2/index/meta.yml
+++ b/software/bwamem2/index/meta.yml
@@ -1,4 +1,4 @@
-name: bwa_index
+name: bwamem2_index
 description: Create BWA-mem2 index for reference genome
 keywords:
     - index
@@ -47,5 +47,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@drpatelh"
     - "@maxulysse"
diff --git a/software/bwamem2/mem/meta.yml b/software/bwamem2/mem/meta.yml
index 2e44951c..7d59b9b4 100644
--- a/software/bwamem2/mem/meta.yml
+++ b/software/bwamem2/mem/meta.yml
@@ -1,4 +1,4 @@
-name: bwa_mem
+name: bwamem2_mem
 description: Performs fastq alignment to a fasta reference using BWA
 keywords:
     - mem
@@ -62,5 +62,4 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    - "@drpatelh"
-    - "@jeremy1805"
+    - "@maxulysse"