Snakefile

import pandas as pd
from snakemake.utils import validate

validate(config, "schema/config.schema.yaml")

units = pd.read_table(config["general"]["units"], index_col=["sample", "unit"],
    dtype=str)
units.index = units.index.set_levels([i.astype(str) for i in units.index.levels])

name_ext = config["general"]["name_ext"][:-1]

def is_single_end(sample, unit):
    return pd.isnull(units.loc[(sample,unit), "fq2"])

if config["general"]["paired_End"]:
    reads = [1,2]
else:
    reads = 1

CONSTRAINT_FILTER = '_constraint_filtered' if config['constraint_filtering']['after_assembly'] else ''
CONSTRAINT_REPAIRED = '_constraint_repaired' if config['constraint_filtering']['repair_after_assembly'] else ''
RES_STR = f"{CONSTRAINT_FILTER}{CONSTRAINT_REPAIRED}"

if config["general"]["in_vivo"]:
    rule all:
        input:
            expand("results/contig_assembly/assemblies/{unit.sample}_{unit.unit}_assembled.fasta", unit=units.reset_index().itertuples())
elif config['constraint_filtering']['repair_after_assembly']:
    rule all:
        input:
            expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_repaired.fasta", unit=units.reset_index().itertuples())
elif config['constraint_filtering']['after_assembly']:
    if config['general']['clustering']:
        rule all:
            input:
                expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_filtered.fastq", unit=units.reset_index().itertuples()),
                expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_cluster.fasta",unit=units.reset_index().itertuples())
    else:
        rule all:
            input:
                expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_filtered.fastq",unit=units.reset_index().itertuples()),
                expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_derep.fasta",unit=units.reset_index().itertuples())
elif config["general"]["clustering"]:
    rule all:
        input:
            expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_cluster.fasta",unit=units.reset_index().itertuples())
else:
    rule all:
        input:
            expand("results/assembly/{unit.sample}_{unit.unit}/{unit.sample}_{unit.unit}_derep.fasta",unit=units.reset_index().itertuples())


ruleorder: assembly > prinseq

include: "rules/demultiplexing.smk"
include: "rules/read_assembly.smk"
include: "rules/dereplication.smk"
include: "rules/constraint_filtering.smk"
include: "rules/contig_assembly.smk"