Merge pull request #299 from qbicsoftware/development

Release 2.16.0

Author: KochTobi

.dependabot/config.yml

@@ -8,10 +8,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up JDK 1.11
+      - name: Set up JDK 1.8
         uses: actions/setup-java@v1
         with:
-          java-version: 1.11
+          java-version: 1.8
 
       - name: Download Checkstyle
         run: wget https://github.com/checkstyle/checkstyle/releases/download/checkstyle-8.31/checkstyle-8.31-all.jar

.github/workflows/java_checkstyle.yml

@@ -8,10 +8,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up JDK 1.11
+      - name: Set up JDK 1.8
         uses: actions/setup-java@v1
         with:
-          java-version: 1.11
+          java-version: 1.8
 
       - name: Load local Maven repository cache
         uses: actions/cache@v2

.github/workflows/run_tests.yml

@@ -88,7 +88,6 @@ This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
 **Deprecated**
 
-
 2.14.0 (2021-10-27)
 -------------------
 

CHANGELOG.rst

@@ -101,7 +101,11 @@ Make sure, that you have defined the Github package Maven repository, in order f
 
 A Nanopore NGS measurement output is delivered to us as a nested folder structure, following this model:
 
-![Nanopore Data Structure Model](./doc/figures/Nanopore_Data_Structure_Model.png)
+![Nanopore Data Structure Model](./doc/figures/Nanopore_Data_Structure_Model.svg)
+
+A more recent model, which places two of the configuration files into a subfolder and adds the barcode alignment file, is also supported:
+
+![Nanopore Data Structure Model v2](./doc/figures/Nanopore_Data_Structure_Model_v2.svg)
 
 #### Nanopore usage example
 

README.md

@@ -81,20 +81,20 @@
       <dependency>
         <groupId>org.codehaus.groovy</groupId>
         <artifactId>groovy-bom</artifactId>
-        <version>2.5.14</version>
+        <version>3.0.9</version>
         <type>pom</type>
         <scope>import</scope>
       </dependency>
-      <dependency>
-        <groupId>org.codehaus.groovy</groupId>
-        <artifactId>groovy-all</artifactId>
-        <version>2.5.14</version>
-        <type>pom</type>
-        <scope>${osgi.scope}</scope>
-      </dependency>
     </dependencies>
   </dependencyManagement>
   <dependencies>
+    <dependency>
+      <groupId>org.codehaus.groovy</groupId>
+      <artifactId>groovy-all</artifactId>
+      <version>3.0.9</version>
+      <type>pom</type>
+      <scope>${osgi.scope}</scope>
+    </dependency>
     <dependency>
       <groupId>org.osgi</groupId>
       <artifactId>osgi.core</artifactId>
@@ -106,12 +106,12 @@
       <groupId>com.github.everit-org.json-schema</groupId>
       <artifactId>org.everit.json.schema</artifactId>
       <version>1.12.2</version>
-      <scope>${osgi.scope}</scope>
+      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>xml-manager-lib</artifactId>
-      <version>1.6.0</version>
+      <version>1.7.0</version>
       <scope>${osgi.scope}</scope>
     </dependency>
     <dependency>
@@ -144,7 +144,7 @@
     <dependency>
       <groupId>org.spockframework</groupId>
       <artifactId>spock-core</artifactId>
-      <version>2.0-groovy-2.5</version>
+      <version>2.0-groovy-3.0</version>
       <scope>test</scope>
     </dependency>
   </dependencies>
@@ -181,7 +181,7 @@
       <plugin>
         <groupId>org.codehaus.gmavenplus</groupId>
         <artifactId>gmavenplus-plugin</artifactId>
-        <version>1.12.1</version>
+        <version>1.13.1</version>
         <executions>
           <execution>
             <goals>
@@ -217,12 +217,12 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-site-plugin</artifactId>
-        <version>3.9.1</version>
+        <version>3.11.0</version>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-project-info-reports-plugin</artifactId>
-        <version>3.1.1</version>
+        <version>3.2.1</version>
       </plugin>
       <plugin>
         <groupId>life.qbic</groupId>
@@ -269,7 +269,7 @@
           <plugin>
             <groupId>biz.aQute.bnd</groupId>
             <artifactId>bnd-maven-plugin</artifactId>
-            <version>5.1.2</version>
+            <version>6.1.0</version>
             <executions>
               <execution>
                 <goals>

doc/figures/Nanopore_Data_Structure_Model.png

@@ -34,7 +34,8 @@ final class OxfordNanoporeExperiment implements ExperimentFolder {
             FQDN_FILES + ".ReportMdLog",
             FQDN_FILES + ".ReportPDFLog",
             FQDN_FILES + ".SequencingSummaryLog",
-            FQDN_FILES + ".ThroughputLog"
+            FQDN_FILES + ".ThroughputLog",
+            FQDN_FILES + ".BarcodeAlignmentLog"
     ]
 
     private final static Set nanoporeFolderTypes = [
@@ -45,7 +46,8 @@ final class OxfordNanoporeExperiment implements ExperimentFolder {
             FQDN_FOLDERS + ".FastQPassFolder",
             FQDN_FOLDERS + ".FastQFailFolder",
             FQDN_FOLDERS + ".UnclassifiedFast5Folder",
-            FQDN_FOLDERS + ".UnclassifiedFastQFolder"
+            FQDN_FOLDERS + ".UnclassifiedFastQFolder",
+            FQDN_FOLDERS + ".OtherReportsFolder"
     ]
 
     private OxfordNanoporeExperiment(String sampleId, List<OxfordNanoporeMeasurement> measurements) {