From f499d5be28877a0379bf22ef5ce3c478d012acdd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Mar 2025 14:15:36 +0100
Subject: [PATCH 1/3] Enable bwa_mem2_directory input datatype

---
 tools/bwa_mem2/bwa-mem2.xml                   |  23 ++++++++++++------
 tools/bwa_mem2/macros.xml                     |  16 +++++++-----
 tools/bwa_mem2/test-data/bwa_mem2_index.loc   |   2 +-
 ...a-mem-mt-genome.fa.0123 => reference.0123} | Bin
 ...bwa-mem-mt-genome.fa.amb => reference.amb} |   0
 ...bwa-mem-mt-genome.fa.ann => reference.ann} |   0
 ...e.fa.bwt.2bit.64 => reference.bwt.2bit.64} | Bin
 ...bwa-mem-mt-genome.fa.pac => reference.pac} | Bin
 8 files changed, 27 insertions(+), 14 deletions(-)
 rename tools/bwa_mem2/test-data/test-cache/{bwa-mem-mt-genome.fa.0123 => reference.0123} (100%)
 rename tools/bwa_mem2/test-data/test-cache/{bwa-mem-mt-genome.fa.amb => reference.amb} (100%)
 rename tools/bwa_mem2/test-data/test-cache/{bwa-mem-mt-genome.fa.ann => reference.ann} (100%)
 rename tools/bwa_mem2/test-data/test-cache/{bwa-mem-mt-genome.fa.bwt.2bit.64 => reference.bwt.2bit.64} (100%)
 rename tools/bwa_mem2/test-data/test-cache/{bwa-mem-mt-genome.fa.pac => reference.pac} (100%)

diff --git a/tools/bwa_mem2/bwa-mem2.xml b/tools/bwa_mem2/bwa-mem2.xml
index 0e26f7956e7..b85402ce03e 100644
--- a/tools/bwa_mem2/bwa-mem2.xml
+++ b/tools/bwa_mem2/bwa-mem2.xml
@@ -281,6 +281,15 @@ bwa-mem2 mem
     </outputs>
 
     <tests>
+        <test>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>
+            <param name="fastq_input_selector" value="paired"/>
+            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            <param name="analysis_type_selector" value="illumina"/>
+            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
+        </test>
         <test>
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
@@ -288,7 +297,7 @@ bwa-mem2 mem
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
+            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -296,7 +305,7 @@ bwa-mem2 mem
             <param name="fastq_input_selector" value="single"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="4" />
+            <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="6" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -305,7 +314,7 @@ bwa-mem2 mem
             <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
+            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -318,7 +327,7 @@ bwa-mem2 mem
             <param name="PL" value="CAPILLARY"/>
             <param name="LB" value="AARDVARK-1" />
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="4" />
+            <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="6" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -328,7 +337,7 @@ bwa-mem2 mem
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
             <param name="output_sort" value="unsorted"/>
-            <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="4" />
+            <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="6" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -338,7 +347,7 @@ bwa-mem2 mem
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
             <param name="output_sort" value="name"/>
-            <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" />
+            <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="6" />
         </test>
         <test>
             <param name="reference_source_selector" value="cached" />
@@ -347,7 +356,7 @@ bwa-mem2 mem
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
+            <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/bwa_mem2/macros.xml b/tools/bwa_mem2/macros.xml
index cdaa0d25899..bc2d1482f4d 100644
--- a/tools/bwa_mem2/macros.xml
+++ b/tools/bwa_mem2/macros.xml
@@ -29,10 +29,14 @@
 
     <token name="@set_reference_fasta_filename@"><![CDATA[
     #if str( $reference_source.reference_source_selector ) == "history":
-        #set $reference_fasta_filename = "localref.fa"
-        ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
-        bwa-mem2 index
-        '${reference_fasta_filename}' &&
+        #if $reference_source.ref_file.is_of_type("bwa_mem2_index"):
+            #set $reference_fasta_filename = $reference_source.ref_file.extra_files_path + "/reference"
+        #else
+            #set $reference_fasta_filename = "localref.fa"
+            ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
+            bwa-mem2 index
+            '${reference_fasta_filename}' &&
+        #end if
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
@@ -59,7 +63,7 @@
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                 <option value="cached">Use a built-in genome index</option>
-                <option value="history">Use a genome from history and build index</option>
+                <option value="history">Use a reference from history and build index if necessary</option>
             </param>
             <when value="cached">
                 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
@@ -71,7 +75,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
+                <param name="ref_file" type="data" format="fasta,bwa_mem2_index" label="Use the following dataset as the reference" help="You can upload a FASTA sequence to the history and use it as reference. For better performance build a reference index separately." />
             </when>
         </conditional>
     </macro>
diff --git a/tools/bwa_mem2/test-data/bwa_mem2_index.loc b/tools/bwa_mem2/test-data/bwa_mem2_index.loc
index db1680c37b1..9f1bc7e738f 100644
--- a/tools/bwa_mem2/test-data/bwa_mem2_index.loc
+++ b/tools/bwa_mem2/test-data/bwa_mem2_index.loc
@@ -1 +1 @@
-mtgenome	mtGenome	Mitochondiral genome	${__HERE__}/test-cache/bwa-mem-mt-genome.fa
\ No newline at end of file
+mtgenome	mtGenome	Mitochondiral genome	${__HERE__}/test-cache/reference
diff --git a/tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.0123 b/tools/bwa_mem2/test-data/test-cache/reference.0123
similarity index 100%
rename from tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.0123
rename to tools/bwa_mem2/test-data/test-cache/reference.0123
diff --git a/tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.amb b/tools/bwa_mem2/test-data/test-cache/reference.amb
similarity index 100%
rename from tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.amb
rename to tools/bwa_mem2/test-data/test-cache/reference.amb
diff --git a/tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.ann b/tools/bwa_mem2/test-data/test-cache/reference.ann
similarity index 100%
rename from tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.ann
rename to tools/bwa_mem2/test-data/test-cache/reference.ann
diff --git a/tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.bwt.2bit.64 b/tools/bwa_mem2/test-data/test-cache/reference.bwt.2bit.64
similarity index 100%
rename from tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.bwt.2bit.64
rename to tools/bwa_mem2/test-data/test-cache/reference.bwt.2bit.64
diff --git a/tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.pac b/tools/bwa_mem2/test-data/test-cache/reference.pac
similarity index 100%
rename from tools/bwa_mem2/test-data/test-cache/bwa-mem-mt-genome.fa.pac
rename to tools/bwa_mem2/test-data/test-cache/reference.pac

From db0b76eefd02d97a591e963b9f554139f8724260 Mon Sep 17 00:00:00 2001
From: Jarvis Lab <jarvislab@itadmins-macbook-pro.local.rockefeller.edu>
Date: Wed, 13 Nov 2024 09:53:10 -0500
Subject: [PATCH 2/3] Add bwa-mem2-idx

---
 tools/bwa_mem2/bwa-mem2-idx.xml | 72 +++++++++++++++++++++++++++++++++
 tools/bwa_mem2/macros-index.xml | 13 ++++++
 2 files changed, 85 insertions(+)
 create mode 100644 tools/bwa_mem2/bwa-mem2-idx.xml
 create mode 100644 tools/bwa_mem2/macros-index.xml

diff --git a/tools/bwa_mem2/bwa-mem2-idx.xml b/tools/bwa_mem2/bwa-mem2-idx.xml
new file mode 100644
index 00000000000..6ed25585f66
--- /dev/null
+++ b/tools/bwa_mem2/bwa-mem2-idx.xml
@@ -0,0 +1,72 @@
+<tool id="bwa_mem2_idx" name="BWA-MEM2-INDEX"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>- creates indexes</description>
+    <macros>
+        <import>macros-index.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+
+## Begin BWA-MEM command line
+echo "Index File runnin" > '$output' &&
+mkdir '$output.files_path' && 
+cd '$output.files_path' &&
+bwa-mem2 index -p 'index' '${input_fasta}'
+    ]]></command>
+
+    <inputs>
+        <param name="input_fasta" type="data" label="Select a genome to index" help="Build an index for this FASTA sequence." format="fasta,fasta.gz"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="text" label="Test Testov"/>
+    </outputs>
+
+    <help><![CDATA[
+**What is does**
+BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
+The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.
+
+The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
+
+-----
+
+**Indices: Selecting reference genomes for BWA**
+
+Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
+
+  1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.
+  2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.
+
+If your genome of interest is not listed here you have two choices:
+
+  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
+  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
+
+-----
+
+**Galaxy-specific option**
+
+Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
+
+  1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
+  2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  <reference index> <PacBio dataset in fastq format>
+  3. *Full list of options*: Allows access to all options through Galaxy interface.
+
+-----
+
+**Bam sorting mode**
+
+The generated bam files can be sorted according to three criteria: coordinates, names and input order.
+
+In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file. 
+
+When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field). 
+
+Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.
+
+
+@RG@
+
+@info@
+    ]]></help>
+</tool>
diff --git a/tools/bwa_mem2/macros-index.xml b/tools/bwa_mem2/macros-index.xml
new file mode 100644
index 00000000000..2ac38cdbe25
--- /dev/null
+++ b/tools/bwa_mem2/macros-index.xml
@@ -0,0 +1,13 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
+        </requirements>
+    </xml>
+
+
+
+    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+</macros>

From 012a51a6794cabebd5fb9d4b1348f4b2354c8d26 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Mar 2025 14:55:28 +0100
Subject: [PATCH 3/3] Use bwa_mem2_index datatype in bwa mem2 indexer

---
 tools/bwa/bwa-mem.xml           |  4 +-
 tools/bwa_mem2/bwa-mem2-idx.xml | 72 +++++++++------------------------
 tools/bwa_mem2/bwa-mem2.xml     |  2 +-
 tools/bwa_mem2/macros-index.xml | 13 ------
 tools/bwa_mem2/macros.xml       |  7 ++--
 5 files changed, 26 insertions(+), 72 deletions(-)
 delete mode 100644 tools/bwa_mem2/macros-index.xml

diff --git a/tools/bwa/bwa-mem.xml b/tools/bwa/bwa-mem.xml
index ed575484968..33b71efbda8 100644
--- a/tools/bwa/bwa-mem.xml
+++ b/tools/bwa/bwa-mem.xml
@@ -6,7 +6,9 @@
         <import>bwa_macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.13">samtools</requirement>
+    </expand>
     <expand macro="stdio"/>
     <command><![CDATA[
 @pipefail@
diff --git a/tools/bwa_mem2/bwa-mem2-idx.xml b/tools/bwa_mem2/bwa-mem2-idx.xml
index 6ed25585f66..e70fc778c51 100644
--- a/tools/bwa_mem2/bwa-mem2-idx.xml
+++ b/tools/bwa_mem2/bwa-mem2-idx.xml
@@ -1,72 +1,36 @@
-<tool id="bwa_mem2_idx" name="BWA-MEM2-INDEX"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>- creates indexes</description>
+<tool id="bwa_mem2_idx" name="BWA-MEM2 indexer"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
+    <description>Build BWA-MEM2 reference index</description>
     <macros>
-        <import>macros-index.xml</import>
+        <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command><![CDATA[
-
-## Begin BWA-MEM command line
-echo "Index File runnin" > '$output' &&
-mkdir '$output.files_path' && 
-cd '$output.files_path' &&
-bwa-mem2 index -p 'index' '${input_fasta}'
+mkdir '$index.extra_files_path' &&
+cd '$index.extra_files_path' &&
+bwa-mem2 index -p 'reference' '${reference}'
     ]]></command>
-
     <inputs>
-        <param name="input_fasta" type="data" label="Select a genome to index" help="Build an index for this FASTA sequence." format="fasta,fasta.gz"/>
+        <param name="reference" type="data" format="fasta,fasta.gz" label="Select a genome to index" help="Build an index for this FASTA sequence."/>
     </inputs>
-
     <outputs>
-        <data name="output" format="text" label="Test Testov"/>
+        <data name="index" format="bwa_mem2_index"/>
     </outputs>
-
+    <tests>
+        <test>
+            <param name="reference" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            <output name="index" ftype="bwa_mem2_index">
+                <extra_files name="reference.0123" type="file" value="test-cache/reference.0123"></extra_files>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
 **What is does**
 BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
 The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.
 
-The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
-
------
-
-**Indices: Selecting reference genomes for BWA**
-
-Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
-
-  1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.
-  2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.
-
-If your genome of interest is not listed here you have two choices:
-
-  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
-  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
-
------
-
-**Galaxy-specific option**
-
-Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
-
-  1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
-  2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  <reference index> <PacBio dataset in fastq format>
-  3. *Full list of options*: Allows access to all options through Galaxy interface.
-
------
-
-**Bam sorting mode**
-
-The generated bam files can be sorted according to three criteria: coordinates, names and input order.
-
-In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file. 
-
-When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field). 
-
-Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.
-
-
-@RG@
+This tools build a reference index for the bwa-mem2 galaxy tool.
 
 @info@
     ]]></help>
+    <expand macro="citations" />
 </tool>
diff --git a/tools/bwa_mem2/bwa-mem2.xml b/tools/bwa_mem2/bwa-mem2.xml
index b85402ce03e..808c1fcbed0 100644
--- a/tools/bwa_mem2/bwa-mem2.xml
+++ b/tools/bwa_mem2/bwa-mem2.xml
@@ -1,4 +1,4 @@
-<tool id="bwa_mem2" name="BWA-MEM2"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="bwa_mem2" name="BWA-MEM2"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
     <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
     <macros>
         <import>read_group_macros.xml</import>
diff --git a/tools/bwa_mem2/macros-index.xml b/tools/bwa_mem2/macros-index.xml
deleted file mode 100644
index 2ac38cdbe25..00000000000
--- a/tools/bwa_mem2/macros-index.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
-        </requirements>
-    </xml>
-
-
-
-    <token name="@TOOL_VERSION@">2.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">21.05</token>
-</macros>
diff --git a/tools/bwa_mem2/macros.xml b/tools/bwa_mem2/macros.xml
index bc2d1482f4d..8b990ce0b71 100644
--- a/tools/bwa_mem2/macros.xml
+++ b/tools/bwa_mem2/macros.xml
@@ -3,6 +3,7 @@
 
     <token name="@TOOL_VERSION@">2.2.1</token>
     <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE_VERSION@">20.01</token>
 
     <xml name="xrefs">
         <xrefs>
@@ -32,7 +33,7 @@
         #if $reference_source.ref_file.is_of_type("bwa_mem2_index"):
             #set $reference_fasta_filename = $reference_source.ref_file.extra_files_path + "/reference"
         #else
-            #set $reference_fasta_filename = "localref.fa"
+            #set $reference_fasta_filename = "localref." + $reference_source.ref_file.extension
             ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
             bwa-mem2 index
             '${reference_fasta_filename}' &&
@@ -45,7 +46,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>
-            <requirement type="package" version="1.13">samtools</requirement>
+            <yield></yield>
         </requirements>
     </xml>
 
@@ -75,7 +76,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta,bwa_mem2_index" label="Use the following dataset as the reference" help="You can upload a FASTA sequence to the history and use it as reference. For better performance build a reference index separately." />
+                <param name="ref_file" type="data" format="fasta,fasta.gz,bwa_mem2_index" label="Use the following dataset as the reference" help="You can upload a FASTA sequence to the history and use it as reference. For better performance build a reference index separately." />
             </when>
         </conditional>
     </macro>