Troubleshoot

Author: standage

microhapulator/tests/test_pipe.py

@@ -70,7 +70,6 @@ def test_pipe_gbr_usc10(tmp_path):
     observed = TypingResult(
         fromfile=tmp_path / "analysis" / "gbr-usc" / "03typing" / "gbr-usc-type.json"
     )
-    assert False
     diff = list(mhapi.diff(observed, expected))
     assert len(diff) == 0
     report = tmp_path / "report" / "report.html"

microhapulator/workflows/preproc-paired.smk

@@ -41,7 +41,7 @@ rule fastqc:
         for end, outfile in enumerate(outfiles, 1):
             outfile = Path(outfile)
             # Snakemake f-strings break with Python 3.12: https://github.com/snakemake/snakemake/issues/2648
-            linkfile = params.outdir + "/R" + end + "-fastqc.html"
+            linkfile = "{}/R{}-fastqc.html".format(params.outdir, end)
             symlink(outfile.name, linkfile)