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binning_wf_template.dag
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### Binning Workflow Begins ###
JOB Mapping ./scripts/01-bowtie.sub
VARS Mapping sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/"
JOB GetDepth ./scripts/02-generate_depths.sub
VARS GetDepth sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/"
JOB GetDepth2 ./scripts/02-generate_depths_maxbin2.sub
VARS GetDepth2 sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/"
JOB Metabat ./scripts/03-metabat.sub
VARS Metabat sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/"
JOB Maxbin ./scripts/04-maxbin2.sub
VARS Maxbin sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/"
JOB Refine ./scripts/05-dastool.sub
VARS Refine sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/"
JOB QA ./scripts/06-checkm.sub
VARS QA sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/" db="CHECKM_DB"
JOB Taxonomy ./scripts/07-gtdbtk.sub
VARS Taxonomy sample="PLACEHOLDER_WORD" location="/staging/NETID_PLACEHOLDER/" db="GTDB_DB"
# Set up the directories before running the first step, mapping.
# Arguments are the base folder, and then the sample name
SCRIPT PRE Mapping ./scripts/set_up.sh /staging/NETID_PLACEHOLDER/ PLACEHOLDER_WORD
### DAG ###
PARENT Mapping CHILD GetDepth
PARENT Mapping CHILD GetDepth2
PARENT GetDepth CHILD Metabat
PARENT GetDepth2 CHILD Maxbin
PARENT Metabat CHILD Refine
PARENT Maxbin CHILD Refine
PARENT Refine CHILD QA
PARENT QA CHILD Taxonomy
SCRIPT POST Taxonomy ./scripts/clean_up.sh /staging/NETID_PLACEHOLDER/ PLACEHOLDER_WORD