Merge pull request #6 from phac-nml/v1.1.3

New SISTR plugin release v1.1.3

README.md

@@ -1,22 +1,16 @@
-# IRIDA SISTR Plugin for Salmonella serotyping
+ # IRIDA SISTR Plugin for Salmonella serotyping
 This new IRIDA plugin allows deployment of SISTR, a tool for *in silico Salmonella* serotyping, in IRIDA platform. For faster and independent updates, SISTR built-in workflow were decided to be ported to plugin format. 
-The analysis report page feature is only available since IRIDA version `20.09`.
-In future SISTR releases we plan to generate reports also in `csv` and `pdf` formats.
-# Features
-New to versions `1.1.1` and `1.1.1b`
 
-* Updated typing databases powered by `SISTR v1.1.1`
-* Reporting of serotyping results via a pretty  web-page (requires `IRIDA >= 20.09`)
-    * More detailed analysis reports for MASH, cgMLST and BLAST profiles
-    * Final results Quality Control checks
-* Plugin versions `1.1.1` and `1.1.1b` are similar with the later supporting `IRIDA v21.01` new metadata update features
+# Features
+* Uses the newest features of the SISTR v1.1.3 including updated nomenclature for O24 and O25 antigens
+* Check if SISTR predicted serovar is in the version 5 list of reportable serovars (https://github.com/phac-nml/sistr_cmd/blob/v1.1.3/sistr/data/serovar-list.txt)
 
 # Building plugin
 Compiled plugin version is available in [`*.jar` folder](/jar/), but you can build your own copy. Building and packaging this code is accomplished using [Apache Maven](http://maven.apache.org/download.cgi). However, you will first need to install [IRIDA](https://github.com/phac-nml/irida) to your local Maven repository. The version of IRIDA you install will have to correspond to the version found in the `irida.version.compiletime` property in the `pom.xml` file of this project. To build successfully plugin there is a need to compile IRIDA corresponding to the version specified in `pom.xml`. 
 Here is a brief workflow to compile new `*.jar` file from the source code 
 
 ```bash
-IRIDA_VERSION=20.09
+IRIDA_VERSION=22.05
 # Build IRIDA dependencies
 git clone https://github.com/phac-nml/irida.git
 git checkout ${IRIDA_VERSION}
@@ -38,11 +32,11 @@ As most IRIDA plugins, this plugin is readily installable by the placement of th
 
 The following dependencies are required to make and run this plugin.
 
-* IRIDA >= 19.01.3 (analysis report rendering feature requires >= 20.09)
-* Java >= 1.8 and Maven >= 3.3.9 (to build IRIDA dependencies)
+* IRIDA >= 19.01.3, <= 24.12 (analysis report rendering feature requires >= 20.09)
+* Java == 11 and Maven >= 3.6.3 (to build IRIDA source code dependencies)
 * Galaxy >= 16.01
 * Shovill == 1.1.0
-* SISTR == 1.1.1
+* SISTR == 1.1.3
 
 # Galaxy configuration
 The plugin assumes a properly configured Galaxy instance that will run the workflow included in the plugin.
@@ -55,11 +49,11 @@ For this version of the plugin, the backend Galaxy instance needs to have the fo
   	* [ToolShed direct link](https://toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0)
 
 
-* SISTR v1.1.1
-	* version 1.1.1
-	* revision 4:17fcac7ddf54
-	* published 2020-08-06
-	* [ToolShed direct link](https://toolshed.g2.bx.psu.edu/view/nml/sistr_cmd/17fcac7ddf54)
+* SISTR v1.1.3
+	* version 1.1.3
+	* revision 6:cf767360ede1
+	* published 2024-12-30
+	* [ToolShed direct link](https://toolshed.g2.bx.psu.edu/view/nml/sistr_cmd/cf767360ede1)
 
 # Gallery
 A couple of illustrations demonstrating plugin in action.
@@ -74,27 +68,30 @@ A couple of illustrations demonstrating plugin in action.
 	* `mash_genome`
 	* `mash_distance`
 	* `qc_messages`
-* update to the newest `shovill` version `1.1.0` with more relaxed assembly setting with minimum contig length of 1bp
+	* `predicted_serovar_in_list`
+* update to the newest `shovill` version `1.1.0` with more relaxed assembly setting with minimum contig length of 1 bp
 
 
 ### Automatic metadata population
-The plugin allows for automatic IRIDA project metadata population and automatic triggering upon sequencing data upload. These features need to be updated in the IRIDA project configuration page.
+The plugin allows for automatic IRIDA project metadata population and automatic triggering upon sequencing data upload. These features need to be updated in the IRIDA project configuration page. Make sure to select on `Save the SISTR generated data (serovar, antigens, etc.) to the project metadata (i.e. Line List tab)? (recommended)` on the parameters screen when launching the pipeline.
 
 <p align="center">
   <img src="./pics/PipelineTile.png">
 </p>
-<p align="center" style="font-style:bold;font-size: 20px">Figure 1: Pipeline Tile</p>
+<p align="center" style="font-style:bold;font-size: 20px"><b>Figure 1:</b> Pipeline Tile</p>
 
 <p align="center">
   <img src="./pics/LineListMeta.png">
 </p>
-<p align="center" style="font-style:bold;font-size: 20px">Figure 2: Key metadata fields populated after serotyping run</p>
+<br>
+<p align="center" style="font-style:bold;font-size: 20px"><b>Figure 2:</b> Key metadata fields populated after serotyping run</p>
 <p align="center"></p>
-
+<br>
 <p align="center">
   <img src="./pics/SISTRViewer.png">
 </p>
-<p align="center" style="font-style:bold;font-size: 20px">Figure 3: Serotyping results rendered by `SISTR Viewer` into a pretty web-page</p>
+<br>
+<p align="center" style="font-style:bold;font-size: 20px"><b>Figure 3:</b> Serotyping results rendered by SISTR Viewer into a pretty web-page</p>
 <p align="center"></p>
 
 

pom.xml

@@ -6,20 +6,20 @@
 
 	<groupId>ca.corefacility.bioinformatics.irida.plugin.serotyping</groupId>
 	<artifactId>sistr-plugin</artifactId>
-	<version>1.1.1b</version>
+	<version>1.1.3</version>
 
 	<!-- Please fill out these properties with information about your particular plugin -->
 	<properties>
 		<!-- Information used to define properties about a plugin. Please see the PF4J docs for more details https://pf4j.org/doc/getting-started.html -->
 		<plugin.id>sistr-plugin</plugin.id>
 		<plugin.class>ca.corefacility.bioinformatics.irida.plugin.serotyping.SISTRplugin</plugin.class>
-		<plugin.version>1.1.1b</plugin.version>
+		<plugin.version>1.1.3</plugin.version>
 		<plugin.provider>Kyrylo Bessonov</plugin.provider>
 		<plugin.dependencies></plugin.dependencies>
 		<plugin.requires.runtime>1.1.0</plugin.requires.runtime>
 
 		<!-- The version of IRIDA your plugin must be compiled against. -->
-		<irida.version.compiletime>21.01</irida.version.compiletime>
+		<irida.version.compiletime>22.05</irida.version.compiletime>
 
 		<!-- Version of the pf4j dependency -->
 		<pf4j.version>2.4.0</pf4j.version>

src/main/java/ca/corefacility/bioinformatics/irida/plugin/serotyping/SISTRSampleUpdater.java

@@ -75,6 +75,8 @@ public class SISTRSampleUpdater implements AnalysisSampleUpdater {
 		.put("mash_distance", "SISTR Genome Match Distance (MASH)")
 		.put("qc_status", "SISTR QC Status")
 		.put("qc_messages", "SISTR QC message(s)")
+		.put("predicted_serovar_in_list", "SISTR reportable serovar?")
+		.put("antigenic_formula", "SISTR antigenic formula")
 		.build();
 			// @formatter:on
 

src/main/java/ca/corefacility/bioinformatics/irida/plugin/serotyping/SISTRplugin.java

@@ -53,7 +53,7 @@ public Optional<String> getAnalysisViewer() {
 
 		@Override
 		public UUID getDefaultWorkflowUUID() {
-			return UUID.fromString("b21ea62c-7916-4ca6-96ba-90c20177b70f");
+			return UUID.fromString("6e5a983d-0259-4e10-b721-88aaf1867ec9");
 		}
 
 		@Override

src/main/resources/workflows/1.1.1/irida_workflow.xml → src/main/resources/workflows/1.1.3/irida_workflow.xml

@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <iridaWorkflow>
-  <id>b21ea62c-7916-4ca6-96ba-90c20177b70f</id>
+  <id>6e5a983d-0259-4e10-b721-88aaf1867ec9</id>
   <name>SISTR</name>
-  <version>1.1.1b</version>
+  <version>1.1.3</version>
   <analysisType>SISTR_TYPING_PLUGIN</analysisType>
   <inputs>
     <sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired>
@@ -18,18 +18,12 @@
     <parameter name="shovill-1-adv.mincov" defaultValue="1">
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="adv.mincov"/>
     </parameter>
-    <parameter name="shovill-1-trim" defaultValue="false">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="trim"/>
-    </parameter>
     <parameter name="shovill-1-adv.namefmt" defaultValue="contig%05d">
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="adv.namefmt"/>
     </parameter>
     <parameter name="shovill-1-adv.depth" defaultValue="100">
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="adv.depth"/>
     </parameter>
-    <parameter name="shovill-1-log" defaultValue="true">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="log"/>
-    </parameter>
     <parameter name="shovill-1-adv.gsize" defaultValue="">
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="adv.gsize"/>
     </parameter>
@@ -46,45 +40,48 @@
       <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" parameterName="assembler"/>
     </parameter>
     <parameter name="sistr_cmd-2-keep_tmp" defaultValue="false">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="keep_tmp"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="keep_tmp"/>
     </parameter>
     <parameter name="sistr_cmd-2-output_format" defaultValue="json">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="output_format"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="output_format"/>
     </parameter>
     <parameter name="sistr_cmd-2-run_mash" defaultValue="true">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="run_mash"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="run_mash"/>
+    </parameter>
+    <parameter name="sistr_cmd-2-serovar_list.selection_mode" defaultValue="default">
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="serovar_list.selection_mode"/>
     </parameter>
     <parameter name="sistr_cmd-2-more_output" defaultValue="-M">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="more_output"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="more_output"/>
     </parameter>
     <parameter name="sistr_cmd-2-verbosity" defaultValue="-vv">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="verbosity"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="verbosity"/>
     </parameter>
     <parameter name="sistr_cmd-2-use_full_cgmlst_db" defaultValue="true">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="use_full_cgmlst_db"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="use_full_cgmlst_db"/>
     </parameter>
     <parameter name="sistr_cmd-2-qc" defaultValue="true">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="qc"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="qc"/>
     </parameter>
     <parameter name="sistr_cmd-2-no_cgmlst" defaultValue="false">
-      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1" parameterName="no_cgmlst"/>
+      <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.3+galaxy0" parameterName="no_cgmlst"/>
     </parameter>
   </parameters>
   <outputs>
+    <output name="shovill-contigs.fasta" fileName="shovill-contigs.fasta"/>
     <output name="shovill-contigs.gfa" fileName="shovill-contigs.gfa"/>
     <output name="shovill-std.log" fileName="shovill-std.log"/>
-    <output name="shovill-contigs.fasta" fileName="shovill-contigs.fasta"/>
+    <output name="sistr-alleles-out.json" fileName="sistr-alleles-out.json"/>
+    <output name="sistr-cgmlst-profiles.csv" fileName="sistr-cgmlst-profiles.csv"/>
     <output name="sistr-novel-alleles.fasta" fileName="sistr-novel-alleles.fasta"/>
     <output name="sistr-predictions" fileName="sistr-predictions.json"/>
-    <output name="sistr-cgmlst-profiles.csv" fileName="sistr-cgmlst-profiles.csv"/>
-    <output name="sistr-alleles-out.json" fileName="sistr-alleles-out.json"/>
   </outputs>
   <toolRepositories>
     <repository>
       <name>sistr_cmd</name>
       <owner>nml</owner>
       <url>https://toolshed.g2.bx.psu.edu</url>
-      <revision>17fcac7ddf54</revision>
+      <revision>cf767360ede1</revision>
     </repository>
     <repository>
       <name>shovill</name>