def build_dag(input_fastqs, chrs=[]):
"""Build a DAG to handle a FASTQ->polymorphic STR loci."""
return DAG().sequence_(
add_(gen_inputs(input_fastqs)),
reduce_([ 'sample', 'readgroup', 'chunk' ], tools.align),
reduce_([ 'sample' ], tools.remdup),
map_(tools.index_bam),
split_([ ('chrom', chrs) ], tools.sputnik),
map_(tools.index_bam, stage_name='Index Sputnik BAMs'),
map_(tools.msitools),
reduce_([ 'sample' ], tools.combine_summaries),
map_(tools.genotyper)
)
from cosmos.Workflow.models import Workflow
from cosmos.contrib.ezflow.dag import DAG, split_,add_,map_,reduce_
from tools import ECHO, CAT, WC, PASTE, Sleep
####################
# Workflow
####################
dag = DAG().sequence_(
add_([ ECHO(tags={'word':'hello'}), ECHO(tags={'word':'world'}) ]),
map_(Sleep),
split_([('i',[1,2])], CAT),
reduce_([], PASTE),
map_(WC),
)
dag.create_dag_img('/tmp/ex.svg')
#################
# Run Workflow
#################
WF = Workflow.start('Example 3',restart=True,delete_intermediates=True)
dag.add_to_workflow(WF)
WF.run()