From c89689b807391bd47d28425d00274613e0512dfa Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 25 Jan 2019 23:48:29 +0100
Subject: [PATCH 1/3] Rename reference to fasta in all cases

---
 main.nf | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index f985d8706..f25ad3e79 100644
--- a/main.nf
+++ b/main.nf
@@ -417,11 +417,12 @@ process makeBWAIndex {
     file "where_are_my_files.txt"
 
     script:
+    base = "${fasta.baseName}"
     """
     mkdir bwa_index
-    cp "${fasta}" bwa_index/
+    mv "${fasta}" "bwa_index/${base}.fasta"
     cd bwa_index
-    bwa index $fasta
+    bwa index "${base}.fasta"
     """
 }
 
@@ -445,13 +446,17 @@ process makeFastaIndex {
     file wherearemyfiles from ch_where_for_fasta_index
 
     output:
-    file "${fasta}.fai" into ch_fasta_faidx_index
-    file "${fasta}"
+    file "faidx/${base}.fasta.fai" into ch_fasta_faidx_index
+    file "faidx/${base}.fasta"
     file "where_are_my_files.txt"
 
     script:
+    base = "${fasta.baseName}"
     """
-    samtools faidx $fasta
+    mkdir faidx
+    mv $fasta "faidx/${base}.fasta"
+    cd faidx
+    samtools faidx "${base}.fasta"
     """
 }
 
@@ -475,12 +480,16 @@ process makeSeqDict {
     file wherearemyfiles from ch_where_for_seqdict
 
     output:
-    file "*.dict" into ch_seq_dict
+    file "seq_dict/*.dict" into ch_seq_dict
     file "where_are_my_files.txt"
 
     script:
+    base = "${fasta.baseName}.fasta"
     """
-    picard CreateSequenceDictionary R=$fasta O="${fasta.baseName}.dict"
+    mkdir -p seq_dict
+    mv $fasta "seq_dict/${base}"
+    cd seq_dict
+    picard CreateSequenceDictionary R=$base O="${fasta.baseName}.dict"
     """
 }
 

From 8c0ec2166ecec5e20ff4cdea8936ee387bbdac78 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 25 Jan 2019 23:51:43 +0100
Subject: [PATCH 2/3] Add changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 420ee26db..11a871f95 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 * [#127](https://github.com/nf-core/eager/pull/127) - Added a second testcase for testing the pipeline properly
 * [#129](https://github.com/nf-core/eager/pull/129) - Support BAM files as [input format](https://github.com/nf-core/eager/issues/41)
+* [#131](https://github.com/nf-core/eager/pull/131) - Support different [reference genome file extensions](https://github.com/nf-core/eager/issues/130)
 
 ### `Fixed`
 * [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors

From 9df93e6f49505e48e4a1350d1881e7bde432809a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 25 Jan 2019 23:52:49 +0100
Subject: [PATCH 3/3] Add docs information on renaming

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index a6ff249e2..8736b4b9e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -168,7 +168,7 @@ If you prefer, you can specify the full path to your reference genome when you r
 ```bash
 --fasta '[path to Fasta reference]'
 ```
-> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`. You may also specify the path to a gzipped (`*.gz` file extension) FastA as reference genome - this will be uncompressed by the pipeline automatically for you.
+> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`. You may also specify the path to a gzipped (`*.gz` file extension) FastA as reference genome - this will be uncompressed by the pipeline automatically for you. Note that other file extensions such as `.fna`, `.fa` are also supported but will be renamed to `.fasta` automatically by the pipeline.
 
 ### `--genome` (using iGenomes)