WIP: unit test for ParallelBaseWrapper ...

bihealth · Feb 22, 2022 · c199440 · c199440
1 parent d49f4fb
commit c199440
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Showing 2 changed files with 70 additions and 2 deletions.
diff --git a/snappy_wrappers/wrapper_parallel.py b/snappy_wrappers/wrapper_parallel.py
@@ -378,7 +378,7 @@ class ParallelBaseWrapper:
     #: don't go further into config dict).
     tool_name = None
     #: The token to use for job names and temporary directories.  Constructed from ``step_name``
-    #: and ``tool_name`` if not specified explicitely here.
+    #: and ``tool_name`` if not specified explicitly here.
     job_name_token = None
     #: The number of bases to pad the parallelization windows with.
     window_padding = 0

diff --git a/tests/snappy_wrappers/test_wrapper_parallel.py b/tests/snappy_wrappers/test_wrapper_parallel.py
@@ -1,9 +1,76 @@
 import pytest
+from snakemake.io import InputFiles, Log, OutputFiles, Params, Resources, Wildcards
+from snakemake.script import Snakemake
+
+from snappy_wrappers.wrapper_parallel import (
+    ParallelBaseWrapper,
+    days,
+    gib,
+    hours,
+    kib,
+    mib,
+    minutes,
+)
+
+
+@pytest.fixture
+def snakemake_obj():
+    """Returns Snakemake object."""
+    # Define helper variables
+    rule_name = "somatic_variant_calling_mutect2_run"
+    threads = 2
+    scriptdir = "/work"
+    input_dict = {
+        "tumor_bai": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam.bai",
+        "tumor_bam": "NGS_MAPPING/output/bwa.P001-T1-DNA1-WGS1/out/bwa.P001-T1-DNA1-WGS1.bam",
+        "normal_bai": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam.bai",
+        "normal_bam": "NGS_MAPPING/output/bwa.P001-N1-DNA1-WGS1/out/bwa.P001-N1-DNA1-WGS1.bam",
+    }
+    output_base_name = "work/bwa.mutect2.P001-T1-DNA1-WGS1/out/bwa.mutect2.P001-T1-DNA1-WGS1"
+    output_dict = {
+        "raw": output_base_name + ".raw.vcf.gz",
+        "raw_md5": output_base_name + ".raw.vcf.gz.md5",
+        "raw_tbi": output_base_name + ".raw.vcf.gz.tbi",
+        "raw_tbi_md5": output_base_name + ".raw.vcf.gz.tbi.md5",
+        "stats": output_base_name + ".raw.vcf.stats",
+        "stats_md5": output_base_name + ".raw.vcf.stats.md5",
+        "f1r2": output_base_name + ".raw.f1r2_tar.tar.gz",
+        "f1r2_md5": output_base_name + ".raw.f1r2_tar.tar.gz.md5",
+    }
+    log_base_name = "work/bwa.mutect2.P001-T1-DNA1-WGS1/log/bwa.mutect2.P001-T1-DNA1-WGS1"
+    log_dict = {
+        "conda_info": log_base_name + ".conda_info.txt",
+        "conda_info_md5": log_base_name + ".conda_info.txt.md5",
+        "conda_list": log_base_name + ".conda_list.txt",
+        "conda_list_md5": log_base_name + ".conda_list.txt.md5",
+        "log": log_base_name + ".log",
+        "log_md5": log_base_name + ".log.md5",
+    }
+    wildcards_dict = {"mapper": "bwa", "tumor_library": "P001-T1-DNA1-WGS1"}
+    params_dict = {"normal_lib_name": "P001-N1-DNA1-WGS1"}
+
+    # Define Snakemake class input
+    input_ = InputFiles(fromdict=input_dict)
+    output_ = OutputFiles(fromdict=output_dict)
+    params_ = Params(fromdict=params_dict)
+    log_ = Log(fromdict=log_dict)
+    wildcards_ = Wildcards(fromdict=wildcards_dict)
+
+    return Snakemake(
+        rulename=rule_name,
+        threads=threads,
+        input_=input_,
+        output=output_,
+        log=log_,
+        params=params_,
+        wildcards=wildcards_,
+        scriptdir=scriptdir,
+    )
 
-from snappy_wrappers.wrapper_parallel import days, gib, hours, kib, mib, minutes
 
 # Test isolated methods ----------------------------------------------------------------------------
 
+
 def test_kib():
     """Tests wrapper_parallel.kib() call."""
     # Define expected dictionary
@@ -100,3 +167,4 @@ def test_days():
         assert actual == expected
 
 
+# Test ParallelBaseWrapper   -----------------------------------------------------------------------