From 9475960928a3ba49624b49ef2b48438a4696ed0f Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Mon, 15 Nov 2021 06:26:01 -0500
Subject: [PATCH] Bwa index (#1040)

* fix a bug that the prefix is not handled by index.

* build the test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bwa/index/main.nf        |  4 ++--
 tests/modules/bwa/index/test.yml | 20 ++++++++++----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf
index 479431ed..db1911cb 100644
--- a/modules/bwa/index/main.nf
+++ b/modules/bwa/index/main.nf
@@ -31,8 +31,8 @@ process BWA_INDEX {
     bwa \\
         index \\
         $options.args \\
-        $fasta \\
-        -p bwa/${fasta.baseName}
+        -p bwa/${fasta.baseName} \\
+        $fasta
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
diff --git a/tests/modules/bwa/index/test.yml b/tests/modules/bwa/index/test.yml
index cdcb5e53..3fe8663d 100644
--- a/tests/modules/bwa/index/test.yml
+++ b/tests/modules/bwa/index/test.yml
@@ -1,16 +1,16 @@
-- name: bwa index
-  command: nextflow run ./tests/modules/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
+- name: bwa index test_bwa_index
+  command: nextflow run tests/modules/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa/index
   files:
-    - path: ./output/bwa/bwa/genome.bwt
-      md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/genome.amb
+    - path: output/bwa/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/genome.sa
-      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: ./output/bwa/bwa/genome.pac
-      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/genome.ann
+    - path: output/bwa/bwa/genome.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1