Add missing required_files to run remotely (#1577)

* Add missing required_files to run remotely

Fix the following error:

```
Fatal error: cannot open file '/jetstream2/scratch/main/jobs/65039573/tool_files/scripts/compare.R': No such file or directory
```

* Replace ubuntu-20.04 runner

https://github.blog/changelog/2025-01-15-github-actions-ubuntu-20-runner-image-brownout-dates-and-other-breaking-changes/

* Lint R scripts

Author: nsoranzo

.github/workflows/pr.yaml

@@ -177,7 +177,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-24.04]
         r-version: ['release']
     steps:
     - uses: actions/checkout@v4

tools/music_deconvolution/macros.xml

@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@VERSION_SUFFIX@">5</token>
     <!-- The ESet inspector/constructor and MuSiC tool can have
          independent Galaxy versions but should reference the same
          package version always. -->

tools/music_deconvolution/music_compare.xml

@@ -31,6 +31,9 @@
     </macros>
     <expand macro="xrefs"/>
     <expand macro="requirements" />
+    <required_files>
+        <include path="scripts/compare.R" />
+    </required_files>
     <command detect_errors="exit_code" ><![CDATA[
 cat '$conf' >> /dev/stderr &&
 mkdir report_data &&

tools/music_deconvolution/music_deconvolution.xml

@@ -6,6 +6,10 @@
     </macros>
     <expand macro="xrefs"/>
     <expand macro="requirements" />
+    <required_files>
+        <include path="scripts/dendrogram.R" />
+        <include path="scripts/estimateprops.R" />
+    </required_files>
     <command detect_errors="exit_code" ><![CDATA[
 cat '$conf' >> /dev/stderr &&
 mkdir report_data &&