Peppy

prjcfg.yaml

@@ -0,0 +1,5 @@
+metadata:
+  sample_table: samples.tsv
+  sample_subtable: units.tsv
+
+snake_config: "config.yaml"

rules/common.smk

@@ -1,17 +1,19 @@
 import pandas as pd
+from peppy import SnakeProject
 from snakemake.utils import validate
 
-report: "../report/workflow.rst"
 
 ###### Config file and sample sheets #####
-configfile: "config.yaml"
+p = SnakeProject("prjcfg_native.yaml")
+configfile: p.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")
 
 # contigs in reference genome

units_peppy.tsv

@@ -0,0 +1,4 @@
+sample_name	platform	fq1	fq2
+A	ILLUMINA	data/reads/a.chr21.1.fq	data/reads/a.chr21.2.fq
+B	ILLUMINA	data/reads/b.chr21.1.fq	data/reads/b.chr21.2.fq
+B	ILLUMINA	data/reads/b.chr21.1.fq