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stolarczyk wants to merge 5 commits into from
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use peppy #22

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750e481
use peppy
stolarczyk Mar 2, 2020
4ebd07d
add PEP config
stolarczyk Mar 2, 2020
e893958
reformat cfg
stolarczyk Mar 2, 2020
25459cb
correct config file path
stolarczyk Mar 3, 2020
adb285c
add pep_version to PEP config
stolarczyk May 21, 2020
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11 changes: 7 additions & 4 deletions rules/common.smk
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Original file line number Diff line number Diff line change
@@ -1,20 +1,23 @@
import pandas as pd
from peppy import Project
from snakemake.utils import validate
from snakemake.utils import min_version

min_version("5.7.1")

report: "../report/workflow.rst"

p = Project(cfg="prjcfg.yaml", sample_table_index="sample",
subsample_table_index=["sample", "unit"])

@stolarczyk stolarczyk Mar 2, 2020

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sample_table_index and subsample_table_index arguments could be skipped if snakemake followed peppy defaults:

  • "sample_name" for sample_table index colnames
  • ["sample_name", "subsample_name"] for subsample_table index colnames

###### Config file and sample sheets #####
configfile: "config.yaml"
configfile: p.config.snake_config
validate(config, schema="../schemas/config.schema.yaml")

samples = pd.read_table(config["samples"]).set_index("sample", drop=False)
samples = p.sample_table
validate(samples, schema="../schemas/samples.schema.yaml")

units = pd.read_table(config["units"], dtype=str).set_index(["sample", "unit"], drop=False)
units.index = units.index.set_levels([i.astype(str) for i in units.index.levels]) # enforce str in index
units = p.subsample_table
validate(units, schema="../schemas/units.schema.yaml")


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