diff --git a/CHANGELOG.md b/CHANGELOG.md index 5695a4af..2bede827 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.8.5] 2024-09-10a + +- Error with packaging subfolders on S3 overlay +- Improved overlay debugging + ## [0.8.4] 2024-09-10 - Fix bug with unrecognized output URIs diff --git a/README.md b/README.md index af534ee4..97aa4dfc 100644 --- a/README.md +++ b/README.md @@ -80,8 +80,8 @@ From the command-line, do, e.g.: ```bash # export NXF_VER=23.04.3 export LOG4J_DEBUG=true # for verbose logging -export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.4/nf-quilt-0.8.4-meta.json -nextflow run main.nf -plugins nf-quilt@0.8.4 +export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.5/nf-quilt-0.8.5-meta.json +nextflow run main.nf -plugins nf-quilt@0.8.5 ``` For Tower, you can use the "Pre-run script" to set the environment variables. diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy index 6720bd0c..ca022c84 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy @@ -136,6 +136,7 @@ class QuiltObserver implements TraceObserver { try { Map overlays = packageOverlays.get(pkgKey, [:]) as Map String relPath = workRelative(source) + log.debug("addOverlay[$relPath] = $source") overlays[relPath] = source packageOverlays[pkgKey] = overlays } finally { @@ -157,7 +158,7 @@ class QuiltObserver implements TraceObserver { for (String key : keys) { log.debug("canOverlayPath: checking key[$key] for $dest") if (dest.toString().contains(key)) { - log.warn("canOverlayPath: matched key[$key] to $dest") + log.debug("canOverlayPath: matched key[$key] to $dest") addOverlay(key, source) return true } @@ -198,7 +199,7 @@ class QuiltObserver implements TraceObserver { outputURIs.each { key, uri -> QuiltPath path = QuiltPathFactory.parse(uri) Map overlays = packageOverlays.get(key, [:]) as Map - // log.debug("onFlowComplete.pkg: $path overlays[${overlays?.size()}]: $overlays") + log.debug("onFlowComplete.pkg: $path overlays[${overlays?.size()}]: $overlays") new QuiltProduct(path, session, overlays) } } diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy index 4ff75f2a..a82f7559 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy @@ -138,7 +138,7 @@ ${nextflow} if (session.isSuccess() || pkg.is_force()) { if (overlays) { - log.info("publishing overlays: ${overlays.size()}") + log.debug("publishing overlays: ${overlays.size()}") publishOverlays(overlays) } else { log.info('No overlays to publish.') diff --git a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF b/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF index 083c1bce..3d68f81b 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: 0.8.4 +Plugin-Version: 0.8.5 Plugin-Provider: Quilt Data Plugin-Requires: >=22.10.6