diff --git a/CHANGELOG.md b/CHANGELOG.md index c4ee7145..3145767a 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/Makefile b/Makefile index 8916f0f8..2257631c 100644 --- a/Makefile +++ b/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/ diff --git a/README.md b/README.md index aad59957..5230217c 100644 --- a/README.md +++ b/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 nf-quilt@0.7.4 +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 nf-quilt@0.7.5 ``` For Tower, you can use the "Pre-run script" to set the environment variables. diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy index 3e52d976..6df35404 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy +++ b/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: $pkg\n") } diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy index 78726f06..24193fa5 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy @@ -244,7 +244,7 @@ class QuiltPackage { builder.setMetadata((ObjectNode)mapper.valueToTree(fullMeta)) Manifest m = builder.build() - + log.debug("QuiltPackage.push", m) m.push(namespace, "nf-quilt:${today()}-${msg}", parsed.workflowName) } diff --git a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF b/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF index c389fb18..622c7d64 100644 --- a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF +++ b/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