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quiltdata · Jan 24, 2024 · 4c01e9d · 4c01e9d
1 parent a1bcd50
commit 4c01e9d
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/Makefile b/Makefile
@@ -3,7 +3,7 @@ PROJECT ?= nf-quilt
 WRITE_BUCKET ?= quilt-example
 FRAGMENT ?= &path=.
 NF_DIR ?= ../nextflow
-NF_BIN ?= ./nextflow
+NF_BIN ?= ./launch.sh
 PID ?= $$$$
 PIPELINE ?= sarek
 QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
@@ -69,7 +69,7 @@ pkg-fail: compile
 	echo "$(TEST_URI)"
 	$(NF_BIN) run ./fail.nf -profile standard -plugins $(PROJECT) --outdir "$(TEST_URI)"
 
-path-input: compile
+path-input: compile-all
 	echo "$(TEST_URI)"
 	$(NF_BIN) run ./main.path.nf -profile standard -plugins $(PROJECT) --outdir "./results"
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -121,7 +121,7 @@ class QuiltPackage {
         this.hash = parsed.getHash()
         this.meta = parsed.getMetadata()
         this.folder = Paths.get(INSTALL_ROOT.toString(), this.toString())
-        //log.debug("QuiltParser.folder[${this.folder}]")
+        log.debug("QuiltPackage.folder[${this.folder}]")
         this.setup()
     }
 
@@ -194,7 +194,9 @@ class QuiltPackage {
             Manifest manifest = namespace.getManifest(resolvedHash)
 
             manifest.install(dest)
-            log.info('done')
+            log.info("done: installed into $dest)")
+            List<String> children = relativeChildren('')
+            log.info("Children: $children")
         } catch (IOException e) {
             log.error("failed to install $packageName")
             // this is non-fatal error, so we don't want to stop the pipeline

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy
@@ -139,7 +139,7 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
 
     @Override
     QuiltPath getPath(String root, String... more) {
-        //log.debug("QuiltFileSystem.getPath`[${root}]: $more")
+        log.debug("QuiltFileSystem.getPath`[${root}]: $more")
 
         QuiltParser p = QuiltParser.forBarePath(root)
         return new QuiltPath(this, p)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -48,7 +48,7 @@ final class QuiltPath implements Path, Comparable {
         this.filesystem = filesystem
         this.parsed = parsed
         this.paths = parsed.getPaths()
-        //log.debug("Creating QuiltPath: $parsed")
+        log.debug("Creating QuiltPath: $parsed [${this.localPath()}]")
     }
 
     String getBucket() {