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Update python and snakemake versions #1

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nh13 opened this issue Jun 24, 2022 · 0 comments · May be fixed by #5
Open

Update python and snakemake versions #1

nh13 opened this issue Jun 24, 2022 · 0 comments · May be fixed by #5

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@nh13
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nh13 commented Jun 24, 2022

We'll need to fix this for loop as snakemake added a "Job Stats" line: https://github.com/fulcrumgenomics/python-snakemake-skeleton/blob/36238b503927dabeeadf3745a051fb6634dadf3a/src/python/pyclient/tests/util.py#L33

fix:

        def fn(d: Dict[str, Any]) -> None:
            if d["level"] != "run_info":
                return
            # NB: skip the first three and two lines
            for counts_line in d["msg"].split("\n")[3:-2]:
                counts_line = counts_line.strip()
                job, count, _, _ = counts_line.split()
                assert int(count) > 0, counts_line

                self.rule_count[job] += int(count)
@ghost ghost mentioned this issue Feb 23, 2023
@jacarey jacarey linked a pull request Feb 23, 2023 that will close this issue
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