Small fix

friendsofstrandseq · Dec 4, 2023 · c89a107 · c89a107
1 parent e90a7a5
commit c89a107
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Showing 3 changed files with 15 additions and 5 deletions.
diff --git a/watchdog_pipeline/watchdog_pipeline.py b/watchdog_pipeline/watchdog_pipeline.py
@@ -39,11 +39,14 @@
 # publishdir_location = "/g/korbel/weber/TMP/WORKFLOW_RESULTS_DEV"
 publishdir_location = "/g/korbel/WORKFLOW_RESULTS"
 genecore_prefix = path_to_watch
-# profile_slurm = ["--profile", "../snakemake_profiles/HPC/dev/slurm_legacy_conda/"]
 profile_slurm = [
     "--profile",
-    "/g/korbel2/weber/workspace/snakemake_profiles/HPC/slurm_EMBL/",
+    "/g/korbel2/weber/workspace/snakemake_profiles/HPC/dev/slurm_legacy_conda/",
 ]
+# profile_slurm = [
+#     "--profile",
+#     "/g/korbel2/weber/workspace/snakemake_profiles/HPC/slurm_EMBL/",
+# ]
 profile_dry_run = [
     "--profile",
     "workflow/snakemake_profiles/local/conda/",
@@ -297,7 +300,9 @@ def check_unprocessed_folder(self):
                                 "PDAC60590MNI",
                                 "DXR30hMaja",
                                 "DXR42hMaja",
-                                "GM19705",
+                                # "GM19705",
+                                "OrgxDoxocx02",
+                                "GM20355x01",
                             ]:
                                 run_id = f"{pipeline}--{plate}--{sample_name}"
                                 workflow_id = self.find_workflow_id_by_name(
@@ -458,6 +463,10 @@ def check_unprocessed_folder(self):
 
                     print(panoptes_entry)
                     print(panoptes_data)
+                    if workflow_id:
+                        assert (
+                            len(panoptes_data) > 0
+                        ), "Data issue between pika & panoptes"
 
                     if panoptes_data:
                         panoptes_data = panoptes_data[0]
@@ -693,7 +702,7 @@ def execute_command(
             "-s",
             "workflow/Snakefile",
             "--set-resources",
-            "ashleys_mark_duplicates:partition=bigmem",
+            "ashleys_mark_duplicates:constraint='milan\|rome'",
             "--config",
             "genecore=True",
             f"genecore_prefix={genecore_prefix}",

diff --git a/workflow/rules/count.smk b/workflow/rules/count.smk
@@ -215,7 +215,7 @@ else:
             "../envs/mc_base.yaml"
         shell:
             """
-            workflow/scripts/normalization/merge-blacklist.py --merge_distance 500000 {input.norm} > {output.merged} 2> {log}
+            cp {input.norm} {ouput.merged}
             """
 
 

diff --git a/workflow/scripts/normalization/merge-blacklist.py b/workflow/scripts/normalization/merge-blacklist.py
@@ -70,6 +70,7 @@ def main():
                     norm_table.loc[[i], "class"] = "good"
                     additional_whitelist += row.end - row.start
 
+
     print("White listing: Removed", additional_whitelist, "bp of sequence for blacklist", file=sys.stderr)
 
     norm_table.to_csv(args.output, index=False, sep="\t")
-Original file line number
+Diff line change
@@ Expand Up / @@ -215,7 +215,7 @@ else: @@
                 "../envs/mc_base.yaml"
             shell:
                 """
-                workflow/scripts/normalization/merge-blacklist.py --merge_distance 500000 {input.norm} > {output.merged} 2> {log}
+                cp {input.norm} {ouput.merged}
                 """
@@ Expand Down @@