workflow directory structure added

workflow/envs/myenv.yaml

+# conda environments needed for the workflow should be stored here.

workflow/report/some-plot.rst

+This plot is colored by {{ snakemake.wildcards.condition }}.

workflow/report/workflow.rst

+Put a description of your workflow here. See [here](https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html) for details.

workflow/rules/common.smk

+from snakemake.utils import validate
+import pandas as pd
+
+# this container defines the underlying OS for each job when using the workflow
+# with --use-conda --use-singularity
+singularity: "docker://continuumio/miniconda3"
+
+##### load config and sample sheets #####
+
+configfile: "config/config.yaml"
+validate(config, schema="../schemas/config.schema.yaml")
+
+samples = pd.read_csv(config["samples"], sep="\t").set_index("sample", drop=False)
+samples.index.names = ["sample_id"]
+validate(samples, schema="../schemas/samples.schema.yaml")

workflow/rules/other.smk

+# An example collection of Snakemake rules imported in the main Snakefile.

workflow/schemas/config.schema.yaml

+$schema: "http://json-schema.org/draft-04/schema#"
+
+description: snakemake configuration file
+
+type: object
+
+# possible entries of the config file and which type they should be
+properties:
+  samples:
+    type: string
+
+# entries that have to be in the config file for successful validation
+required:
+  - samples

workflow/schemas/samples.schema.yaml

+$schema: "http://json-schema.org/draft-04/schema#"
+
+description: an entry in the sample sheet
+
+# columns that the config/samples.tsv file can have and which type they should be
+properties:
+  sample:
+    type: string
+    description: sample name/identifier
+  condition:
+    type: string
+    description: sample condition that will be compared during differential analysis (e.g. a treatment, a tissue time, a disease)
+
+# columns that the config/samples.tsv file must have to pass schema validation
+required:
+  - sample
+  - condition

workflow/scripts/common.py

+# Any Python script in the scripts folder will be able to import from this module.