Merge pull request #126 from CCBR/spooker

Run spooker on workflow completion

CHANGELOG.md

@@ -1,3 +1,7 @@
+## development version
+
+- Run spooker on workflow completion (#126).
+
 ## CHAMPAGNE 0.2.0
 
 ### New features

MANIFEST.in

@@ -1,6 +1,7 @@
 recursive-include assets
 recursive-include bin
 recursive-include conf
+recursive-include lib
 recursive-include modules
 recursive-include src
 recursive-include submodules

lib/Utils.groovy

@@ -0,0 +1,21 @@
+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} ${pipeline_name}"
+        def out = new StringBuilder()
+        def err = new StringBuilder()
+        try {
+            def command = command_string.execute()
+            command.consumeProcessOutput(out, err)
+            command.waitFor()
+        } catch(IOException e) {
+            err = e
+        }
+        new FileWriter("${workflow.launchDir}/log/spooker.log").with {
+            write("${out}\n${err}")
+            flush()
+        }
+        return err
+    }
+}

main.nf

@@ -35,6 +35,14 @@ include { PPQT_PROCESS
           MULTIQC                  } from "./modules/local/qc.nf"
 include { NORMALIZE_INPUT          } from "./modules/local/deeptools.nf"
 
+workflow.onComplete {
+    println "Running spooker"
+    def message = Utils.spooker(workflow)
+    if (message) {
+        println message
+    }
+}
+
 workflow MAKE_REFERENCE {
     PREPARE_GENOME()
 }

pyproject.toml

@@ -60,7 +60,7 @@ Changelog = "https://github.com/CCBR/CHAMPAGNE/blob/main/docs/CHANGELOG.md"
 champagne = "."
 
 [tool.setuptools.package-data]
-"*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/**", "bin/**", "conf/**", "modules/**", "subworkflows/**", "tests/**"]
+"*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/**", "bin/**", "conf/**", "lib/**", "modules/**", "subworkflows/**", "tests/**"]
 
 [tool.setuptools.dynamic]
 version = {file = "VERSION"}