diff --git a/watchdog_pipeline/watchdog_pipeline.py b/watchdog_pipeline/watchdog_pipeline.py index 4c1a6614..ea647898 100644 --- 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 index f1a0e74e..7eee69bb 100755 --- 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 index 750d3966..998c9650 100755 --- 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")