Merge pull request #49 from CCBR/fix-spooker

fix spooker call: parse workflow attributes outside groovy function

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
 

bin/crispin

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+TOOLDIR=$(realpath $(dirname $(dirname ${BASH_SOURCE})))
+
+${TOOLDIR}/main.py "$@"

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()
         }

main.nf

@@ -27,8 +27,10 @@ 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}"
+        println "Running: spooker $launch_dir $pipeline_name"
+        def message = Utils.spooker(launch_dir, pipeline_name)
         if (message) {
             println message
         }

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())