From f5ed7c96a5b530ed42348458cfff9990a9fa769d Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 16 Oct 2024 12:00:31 -0400
Subject: [PATCH 1/3] fix: parse workflow attributes outside groovy function

---
 bin/crispin      |  5 +++++
 lib/Utils.groovy |  7 +++----
 main.nf          |  4 +++-
 main.py          | 16 ++++++++++++++++
 4 files changed, 27 insertions(+), 5 deletions(-)
 create mode 100755 bin/crispin
 create mode 100755 main.py

diff --git a/bin/crispin b/bin/crispin
new file mode 100755
index 0000000..8fcdf75
--- /dev/null
+++ b/bin/crispin
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+TOOLDIR=$(realpath $(dirname $(dirname ${BASH_SOURCE})))
+
+${TOOLDIR}/main.py "$@"
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
index db78a83..acae2da 100644
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -1,8 +1,7 @@
 class Utils {
     // run spooker for the workflow
-    public static String spooker(workflow) {
-        def pipeline_name = "${workflow.manifest.name.tokenize('/')[-1]}"
-        def command_string = "spooker ${workflow.launchDir} ${pipeline_name}"
+    public static String spooker(launch_dir, pipeline_name) {
+        def command_string = "spooker ${launch_dir} ${pipeline_name}"
         def out = new StringBuilder()
         def err = new StringBuilder()
         try {
@@ -12,7 +11,7 @@ class Utils {
         } catch(IOException e) {
             err = e
         }
-        new FileWriter("${workflow.launchDir}/log/spooker.log").with {
+        new FileWriter("${launch_dir}/log/spooker.log").with {
             write("${out}\n${err}")
             flush()
         }
diff --git a/main.nf b/main.nf
index b2d4d30..f808523 100644
--- a/main.nf
+++ b/main.nf
@@ -28,7 +28,9 @@ include { DRUGZ } from './modules/local/drugz.nf'
 workflow.onComplete {
     if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
         println "Running spooker"
-        def message = Utils.spooker(workflow)
+        def pipeline_name = "${workflow.manifest.name.tokenize('/')[-1]}"
+        def launch_dir = "${workflow.launchDir}"
+        def message = Utils.spooker(launch_dir, pipeline_name)
         if (message) {
             println message
         }
diff --git a/main.py b/main.py
new file mode 100755
index 0000000..2b8c3f7
--- /dev/null
+++ b/main.py
@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+import os
+import re
+import sys
+
+# add script directory to the path to allow champagne CLI to work out-of-the-box
+# without the need to install it via pip first
+SCRIPT_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")
+sys.path.append(SCRIPT_DIR)
+from src.__main__ import main
+
+if (
+    __name__ == "__main__"
+):  # this block is adapted from the executable file created by `pip install`
+    sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0])
+    sys.exit(main())

From 8f8ef6b44093718a9c65c5b70f821d2811a5ae53 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 16 Oct 2024 14:19:37 -0400
Subject: [PATCH 2/3] chore: update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ee73188..a88e028 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
 ## CRISPIN development version
 
 - CRISPIN is now archived in Zenodo as v1.0.0. You can cite it with <https://doi.org/10.5281/zenodo.13844209>. (@kelly-sovacool)
+- Fix bug in spooker handler. (#49, @kelly-sovacool)
 
 ## CRISPIN 1.0.0
 

From 77168a158dc15836d87931e1154694a222109ec4 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 16 Oct 2024 14:24:06 -0400
Subject: [PATCH 3/3] style: print spooker command

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index f808523..602266c 100644
--- a/main.nf
+++ b/main.nf
@@ -27,9 +27,9 @@ include { DRUGZ } from './modules/local/drugz.nf'
 
 workflow.onComplete {
     if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
-        println "Running spooker"
         def pipeline_name = "${workflow.manifest.name.tokenize('/')[-1]}"
         def launch_dir = "${workflow.launchDir}"
+        println "Running: spooker $launch_dir $pipeline_name"
         def message = Utils.spooker(launch_dir, pipeline_name)
         if (message) {
             println message