diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy index 23b39013..c57a7ef0 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy @@ -295,6 +295,7 @@ ${nextflow} String[] wildcards = summarize.split(',') wildcards.each { wildcard -> List paths = match(wildcard) + log.debug("setupSummarize: ${paths.size()} matches for ${wildcard}") paths.each { path -> String filename = path.getFileName() Map entry = ['path': path.toString(), 'title': filename] 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 fbd9b561..122b0121 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy @@ -81,11 +81,15 @@ class QuiltPackage { } static QuiltPackage forParsed(QuiltParser parsed) { + log.debug("QuiltPackage.forParsed: $parsed") def pkgKey = parsed.toPackageString() def pkg = PKGS.get(pkgKey) + log.debug("QuiltPackage.forParsed: $pkgKey -> $pkg") if (pkg) { return pkg } + log.debug('QuiltPackage.forParsed: new') pkg = new QuiltPackage(parsed) + log.debug("QuiltPackage.forParsed: -> $pkg") PKGS[pkgKey] = pkg return pkg } @@ -95,6 +99,7 @@ class QuiltPackage { } static boolean deleteDirectory(Path rootPath) { + log.debug 'deleteDirectory' try { if (!Files.exists(rootPath)) { return false } } @@ -162,7 +167,7 @@ class QuiltPackage { void setup() { Files.createDirectories(this.folder) this.installed = false - install() // FIXME: only needed for nextflow < 23.12? + //install() // FIXME: only needed for nextflow < 23.12? } boolean is_force() { @@ -211,6 +216,7 @@ class QuiltPackage { // /does-files-createtempdirectory-remove-the-directory-after-jvm-exits-normally void recursiveDeleteOnExit() throws IOException { Path path = packageDest() + log.debug("recursiveDeleteOnExit: ${path}") Files.walkFileTree(path, new SimpleFileVisitor() { @Override @@ -233,10 +239,11 @@ class QuiltPackage { Namespace namespace = registry.getNamespace(packageName) Manifest.Builder builder = Manifest.builder() + Path dest = packageDest() - Files.walk(packageDest()).filter(f -> Files.isRegularFile(f)).forEach(f -> { - log.debug("push: ${f} -> ${packageDest()}") - String logicalKey = packageDest().relativize(f) + Files.walk(dest).filter(f -> Files.isRegularFile(f)).forEach(f -> { + log.debug("push: ${f} -> ${dest}") + String logicalKey = dest.relativize(f) LocalPhysicalKey physicalKey = new LocalPhysicalKey(f) long size = Files.size(f) builder.addEntry(logicalKey, new Entry(physicalKey, size, null, null))