def run_qc(config, jobs, out_dir, no_conda, dryrun, snakemake_args):
"""Runs the ATLAS Quality control protocol, the first step of the workflow.
A skeleton configuration file can be generated with defaults using:
\b
atlas make-config
For more details, see: http://pnnl-atlas.readthedocs.io/
"""
run_workflow(os.path.realpath(config), jobs, out_dir, no_conda, dryrun, snakemake_args,workflow="qc")
def run_annotate(config, jobs, out_dir, no_conda, dryrun, snakemake_args):
"""Runs the ATLAS annotation protocol on assembled contigs. If FASTQ files are provided
for a sample, quantification is also performed.
A skeleton configuration file can be generated using:
\b
atlas make-config
For more details, see: http://pnnl-atlas.readthedocs.io/
"""
run_workflow(os.path.realpath(config), jobs, out_dir, no_conda, dryrun, snakemake_args,workflow="annotate")
def run_assemble(config, jobs, out_dir, no_conda, dryrun, snakemake_args):
"""Runs the complete ATLAS protocol from raw reads through assembly, annotation, quantification,
and genomic binning.
A skeleton configuration file can be generated with defaults using:
\b
atlas make-config
For more details, see: http://pnnl-atlas.readthedocs.io/
"""
run_workflow(os.path.realpath(config), jobs, out_dir, no_conda, dryrun, snakemake_args,workflow="complete")
def run_binner(config, jobs, out_dir, no_conda, dryrun, snakemake_args):
"""Runs the ATLAS binner protocol. Output can be found in <output directory>/genomes
bins contigs using different binners, estimates completeness and contamination
for each bin. Dereplicate bins for all samples and select the best genome for each species.
Calculate abundance of different species per genome.
run after 'atlas assemble'
For more details, see: http://pnnl-atlas.readthedocs.io/
"""
run_workflow(
os.path.realpath(config),
jobs,
out_dir,
no_conda,
dryrun,
snakemake_args,
workflow="binning",
)