Troubleshoot

Author: standage

microhapulator/tests/test_pipe.py

@@ -67,7 +67,6 @@ def test_pipe_gbr_usc10(tmp_path):
     args = microhapulator.cli.get_parser().parse_args(arglist)
     microhapulator.cli.pipe.main(args)
     expected = SimulatedProfile(fromfile=data_file("prof/gbr-usc10-sim.json"))
-    print("DEBUGger", *list((tmp_path / "analysis" / "gbr-usc" / "03typing").glob("*")), sep="\n")
     observed = TypingResult(
         fromfile=tmp_path / "analysis" / "gbr-usc" / "03typing" / "gbr-usc-type.json"
     )

microhapulator/workflows/preproc-paired.smk

@@ -40,7 +40,8 @@ rule fastqc:
         outfiles = sorted(Path(params.outdir).glob("*.html"))
         for end, outfile in enumerate(outfiles, 1):
             outfile = Path(outfile)
-            linkfile = f"{params.outdir}/R{end}-fastqc.html"
+            # Snakemake f-strings break with Python 3.12: https://github.com/snakemake/snakemake/issues/2648
+            linkfile = params.outdir + "/R" + end + "-fastqc.html"
             symlink(outfile.name, linkfile)