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Commit 9444376f authored by Susheel Busi's avatar Susheel Busi
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Merge branch 'work' into 'master'

cleaner snakefile for workflow

See merge request susheel.busi/ont_pilot_gitlab!64
parents 3f3bbc8b d2bb2244
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1 merge request!64cleaner snakefile for workflow
# File for running ONT analyses
# default configuration file
configfile:"config/CONFIG.yaml"
# default executable for snakmake
shell.executable("bash")
# input settings
RUNS=config['runs']['first']
STEPS=config['steps']
# include rules for the workflows based on "steps" in the CONFIG.yaml file
# ONT analyses workflow
TARGETS = []
if 'assembly_annotation' in STEPS:
include: "workflows/assembly_annotation.smk"
TARGETS += ["assemble_and_coverage.done",
"annotate.done",
"basecall_merge_qc.done",
"coverage_of_references.done",
"prodigal_gene_call.done",
"diamond_proteins.done"]
if 'mmseq' in STEPS:
include: "workflows/mmseq.smk"
TARGETS += ["mmseq_comparison_for_ont.done"]
if 'metaT' in STEPS:
include: "workflows/metat.smk"
TARGETS += ["metaT_mapping_for_ONT.done"]
if 'mapping' in STEPS:
include: "workflows/mapping.smk"
TARGETS += ["mapping_for_binning.done"]
if 'binning' in STEPS:
include: "workflows/binning.smk"
TARGETS += ["binning_for_ont.done"]
if 'taxonomy' in STEPS:
include: "workflows/taxonomy.smk"
TARGETS += ["taxonomy_for_ont.done"]
else:
raise Exception('You are not serious. No input data')
rule all:
input:
TARGETS
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