diff --git a/.gitignore b/.gitignore
index d832e231..07c0144a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,5 +2,4 @@
 work/
 data/
 results/
-tools/bwa/mem_ignore
 .DS_Store
diff --git a/tools/bwa/mem/meta.yml b/tools/bwa/mem/meta.yml
index 4f8fe44d..1887cd38 100644
--- a/tools/bwa/mem/meta.yml
+++ b/tools/bwa/mem/meta.yml
@@ -15,19 +15,18 @@ input:
     -
         - id:
             type: val
-            description: read id for paired-end sequences
+            description: read/read pair id
         - reads:
             type: file
             description: Input fastq file
             pattern: *.{fastq,fq}
-        - genome:
-            type: file
-            description: Input fasta reference genome
-            pattern: *.{fasta,fa}
         - index:
             type: file
             description: bwa indexes file
             pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
+        - prefix:
+            type: val
+            description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
 output:
     -
         - bam: