Esempio n. 1
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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)
    )
Esempio n. 2
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File: ex3.py Progetto: jluquette/msi
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()
Esempio n. 3
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File: ex2.py Progetto: jluquette/msi
from cosmos.Workflow.models import Workflow
from cosmos.contrib.ezflow.dag import DAG, split_,add_,map_,reduce_
from tools import ECHO, CAT, WC, PASTE

####################
# Workflow
####################

dag = DAG().sequence_(
    add_([ ECHO(tags={'word':'hello'}), ECHO(tags={'word':'world'}) ]),
    split_([('i',[1,2])], CAT),
    reduce_([], PASTE),
    map_(WC)
)

dag.create_dag_img('/tmp/ex.svg')

#################
# Run Workflow
#################

WF = Workflow.start('Example 2',restart=True,delete_intermediates=True)
dag.add_to_workflow(WF)
WF.run()