fixes mosdepth and somalier errors

src/run_quac.py

@@ -216,7 +216,7 @@ if __name__ == "__main__":
         help="Flag to run the snakemake locally and not as a Slurm job. "
         "Useful for testing purposes.",
     )
-    RERUN_FAILED_DEFAULT = 1
+    RERUN_FAILED_DEFAULT = 0
     WRAPPER.add_argument(
         "--rerun_failed",
         help=f"Number of times snakemake restarts failed jobs. This may be set to >0 "

workflow/rules/coverage_analysis.smk

@@ -50,14 +50,13 @@ rule mosdepth_plot:
         "mosdepth"
     params:
         in_dir = lambda wildcards, input: Path(input[0]).parent,
-        workflow_dir = Path(workflow.basedir).parent
     shell:
         r"""
         echo "Heads up: Mosdepth-plotting is run on all samples in "{params.in_dir}"; Not just the files mentioned in the rule's input."
 
         cd {params.in_dir}  # if not in directory, mosdepth uses filepath as sample name :(
         python {input.script} \
-            --output {params.workflow_dir}/{output} \
+            --output {output} \
             *.mosdepth.global.dist.txt
         """
 

workflow/rules/relatedness_ancestry.smk

@@ -84,7 +84,7 @@ rule somalier_ancestry:
         {input.somalier_tool} ancestry \
             --output-prefix {params.outdir}/somalier \
             --labels {input.labels_1kg} \
-            {input.somalier_1kg}*.somalier ++ \
+            {input.somalier_1kg}/*.somalier ++ \
             {params.indir}/*.somalier \
             > {log} 2>&1
         """