fix: display wrapper or external script code in report #1393 (#1404)

* Remove the decode attributes of source files fix #1393

* Adding a test with report generation without md5sum check

* Formatting with black

* feat: Adding --cluster-cancel and --cluster-cancel-nargs (#1395)

* Adding support for --cluster-[m]cancel

* Adding support for --cluster-[m]cancel.

* Adressing points from code review

* [ci skip] fix typos

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
Co-authored-by: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

snakemake/report/__init__.py

@@ -263,7 +263,7 @@ def code(self):
             _, source, language, _ = script.get_source(
                 self._rule.script, self._rule.workflow.sourcecache, self._rule.basedir
             )
-            sources = [source.decode()]
+            sources = [source]
         elif self._rule.wrapper is not None and not contains_wildcard(
             self._rule.wrapper
         ):
@@ -276,7 +276,7 @@ def code(self):
                 ),
                 self._rule.workflow.sourcecache,
             )
-            sources = [source.decode()]
+            sources = [source]
         elif self._rule.notebook is not None and not contains_wildcard(
             self._rule.notebook
         ):

tests/test_report_display_code/Snakefile

@@ -0,0 +1,30 @@
+rule all:
+    input:
+        "test.vcf.gz",
+
+
+rule a:
+    output:
+        "{prefix}.txt",
+    shell:
+        "touch {output}"
+
+
+rule b:
+    input:
+        "{prefix}.txt",
+    output:
+        "{prefix}.vcf",
+    script:
+        "test.py"
+
+
+rule bgzip:
+    input:
+        "{prefix}.vcf",
+    output:
+        "{prefix}.vcf.gz",
+    log:
+        "logs/bgzip/{prefix}.log",
+    wrapper:
+        "v1.1.0/bio/bgzip"

tests/test_report_display_code/test.py

@@ -0,0 +1,2 @@
+with open(snakemake.output[0], "w") as f:
+    f.write("bar")

tests/tests.py

@@ -229,6 +229,14 @@ def test_report_dir():
     run(dpath("test_report_dir"), report="report.zip", check_md5=False)
 
 
+def test_report_display_code():
+    run(
+        dpath("test_report_display_code"),
+        report="report.html",
+        check_md5=False,
+    )
+
+
 def test_dynamic():
     run(dpath("test_dynamic"))