Incorporating changes from code review

bihealth · Dec 13, 2022 · 1912333 · 1912333
1 parent e9bf5c3
commit 1912333
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Showing 4 changed files with 5 additions and 8 deletions.
diff --git a/snappy_pipeline/workflows/ngs_mapping/Snakefile b/snappy_pipeline/workflows/ngs_mapping/Snakefile
@@ -169,7 +169,7 @@ rule ngs_mapping_minimap2_run:
     output:
         **wf.get_output_files("minimap2", "run"),
     threads: wf.get_resource("minimap2", "run", "threads")
-    params:
+    resources:
         time=wf.get_resource("minimap2", "run", "time"),
         memory=wf.get_resource("minimap2", "run", "memory"),
         partition=wf.get_resource("minimap2", "run", "partition"),

diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py
@@ -663,7 +663,7 @@ def get_resource_usage(self, action):
         mem_gb = int(3.5 * self.config["minialign"]["mapping_threads"])
         return ResourceUsage(
             threads=self.config["minialign"]["mapping_threads"],
-            time="0-12:00:00",  # 2 days
+            time="2-00:00:00",  # 2 days
             memory=f"{mem_gb}G",
         )
 

diff --git a/snappy_pipeline/workflows/wgs_sv_calling/__init__.py b/snappy_pipeline/workflows/wgs_sv_calling/__init__.py
@@ -92,7 +92,8 @@
 
 - ``"dna_long"`` (PacBio)
     - ``"pb_honey_spots"``
-    - ``"sniffles"``, ``"sniffles2"``
+    - ``"sniffles"``
+    - ``"sniffles2"``
 
 =======
 Reports
@@ -172,7 +173,7 @@
       num_threads: 16
     sniffles2:
       num_threads: 16
-      tandem_repeats: /fast/groups/cubi/work/projects/biotools/sniffles2/trf/GRCh37/human_hs37d5.trf.bed
+      tandem_repeats: /fast/groups/cubi/work/projects/biotools/sniffles2/trf/GRCh37/human_hs37d5.trf.bed  # REQUIRED
 """
 
 

diff --git a/snappy_wrappers/wrappers/minimap2/wrapper.py b/snappy_wrappers/wrappers/minimap2/wrapper.py
@@ -11,10 +11,6 @@
 seq_platform = snakemake.params.args["extra_infos"]["seqPlatform"]
 library_kit = snakemake.params.args["extra_infos"]["libraryKit"]
 
-import pdb
-
-pdb.set_trace()
-
 shell(
     r"""
 set -x