From c67e591caf07ae5662dd00f0dd5c3ecee488d65a Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Sat, 20 Feb 2021 12:51:01 +0100
Subject: [PATCH] apply suggestions from review

thanks @drpatelh
---
 software/bwameth/align/main.nf        |  4 +++-
 software/bwameth/align/meta.yml       |  3 ---
 software/bwameth/index/main.nf        |  4 ++--
 tests/software/bwameth/index/test.yml | 12 ++++++------
 4 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/software/bwameth/align/main.nf b/software/bwameth/align/main.nf
index cdfb48b7..14ac1b0b 100644
--- a/software/bwameth/align/main.nf
+++ b/software/bwameth/align/main.nf
@@ -31,11 +31,13 @@ process BWAMETH_ALIGN {
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
+    INDEX=`find -L ./ -name "*bwameth.c2t" | sed 's/.bwameth.c2t//'`
+
     bwameth.py \\
         $options.args \\
         $read_group \\
         -t $task.cpus \\
-        --reference ${index}/genome.fa \\
+        --reference \$INDEX \\
         $reads \\
         | samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
 
diff --git a/software/bwameth/align/meta.yml b/software/bwameth/align/meta.yml
index d5234f4d..9d46e4cc 100644
--- a/software/bwameth/align/meta.yml
+++ b/software/bwameth/align/meta.yml
@@ -54,9 +54,6 @@ input:
     - index:
         type: dir
         description: Directory containing bwameth genome index
-    - fasta:
-        type: file
-        description: Input genome fasta file
 output:
     - meta:
         type: map
diff --git a/software/bwameth/index/main.nf b/software/bwameth/index/main.nf
index a5587371..1468e15c 100644
--- a/software/bwameth/index/main.nf
+++ b/software/bwameth/index/main.nf
@@ -19,10 +19,10 @@ process BWAMETH_INDEX {
     }
 
     input:
-    path fasta, stageAs: "index/genome.fa"
+    path fasta, stageAs: "bwameth/*"
 
     output:
-    path "index"        , emit: index
+    path "bwameth"      , emit: index
     path "*.version.txt", emit: version
 
     script:
diff --git a/tests/software/bwameth/index/test.yml b/tests/software/bwameth/index/test.yml
index 2b45c718..dac20ada 100644
--- a/tests/software/bwameth/index/test.yml
+++ b/tests/software/bwameth/index/test.yml
@@ -4,15 +4,15 @@
     - bwameth
     - bwameth_index
   files:
-    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.pac
+    - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.pac
       md5sum: 7586c6a3be45c4dea15376a5c7bb9bf0
-    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.amb
+    - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.amb
       md5sum: 87e019665cbb66bdee2bacccb26845c9
-    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.ann
+    - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.ann
       md5sum: a4659a63572b6998c67457bd8e95790d
-    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.bwt
+    - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.bwt
       md5sum: 582854008bcbe99d5b51290773a7db5f
-    - path: ./output/bwameth/index/genome.fa.bwameth.c2t
+    - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t
       md5sum: db670853725f4a31080c991e9df6b330
-    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.sa
+    - path: ./output/bwameth/bwameth/genome.fa.bwameth.c2t.sa
       md5sum: 020db07e7e1544dc961c30c9936f3213