Multiqc (#153)

Find all multiqc_report.html files

.gitignore

@@ -29,3 +29,5 @@ gradle-app.setting
 *.icloud
 params.yaml
 *.old
+null
+quilt+*

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.7.5] 2023-10-17
+
+- Grab all multiqc subfolders
+
 ## [0.7.4] 2023-10-16b
 
 - Actually print the exception stack trace

Makefile

@@ -87,7 +87,7 @@ deps:
 refresh:
 	./gradlew --refresh-dependencies dependencies
 
-install:
+install: compile
 	./gradlew copyPluginZip
 	rm -rf ${HOME}/.nextflow/plugins/$(PROJECT)-${VERSION}
 	cp -r build/plugins/$(PROJECT)-${VERSION} ${HOME}/.nextflow/plugins/

README.md

@@ -75,8 +75,8 @@ From the command-line, do, e.g.:
 
 ```bash
 # export NXF_VER=23.04.3
-export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.4/nf-quilt-0.7.4-meta.json
-nextflow run main.nf -plugins [email protected].4
+export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.5/nf-quilt-0.7.5-meta.json
+nextflow run main.nf -plugins [email protected].5
 ```
 
 For Tower, you can use the "Pre-run script" to set the environment variables.

plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy

@@ -80,7 +80,7 @@ ${nextflow}
 
 `${meta['workflow']['stats']['processes']}`
 '''
-    private final static String DEFAULT_SUMMARIZE = '*.md,*.html,*.?sv,*.pdf,multiqc/multiqc_report.html'
+    private final static String DEFAULT_SUMMARIZE = '*.md,*.html,*.?sv,*.pdf,igv.json,**/multiqc_report.html'
 
     private final static String[] BIG_KEYS = [
         'nextflow', 'commandLine', 'scriptFile', 'projectDir',
@@ -143,7 +143,9 @@ ${nextflow}
         }
         catch (Exception e) {
             log.error("publish failed:", e)
-            throw e
+            print("FAILED: $pkg\n")
+            return
+            // throw e
         }
         print("SUCCESS: $pkg\n")
     }

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy

@@ -244,7 +244,7 @@ class QuiltPackage {
         builder.setMetadata((ObjectNode)mapper.valueToTree(fullMeta))
 
         Manifest m = builder.build()
-
+        log.debug("QuiltPackage.push", m)
         m.push(namespace, "nf-quilt:${today()}-${msg}", parsed.workflowName)
     }
 

plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.7.4
+Plugin-Version: 0.7.5
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=22.10.6