Commit 394bdf80 authored by AntonieV's avatar AntonieV
Browse files

workflow directory structure added

parent 8c6bb66f
# conda environments needed for the workflow should be stored here.
This plot is colored by {{ snakemake.wildcards.condition }}.
Put a description of your workflow here. See [here](https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html) for details.
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")
# An example collection of Snakemake rules imported in the main Snakefile.
$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
$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
# Any Python script in the scripts folder will be able to import from this module.
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