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Commit 98955ae9 authored by Valentina Galata's avatar Valentina Galata
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updated step analysis

parent a020fdeb
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1 merge request!76Merge "cleanup" branch with "master" branch
......@@ -10,8 +10,8 @@ from tempfile import TemporaryDirectory
# configfile:"config/CONFIG.yaml"
# Paths
SRC_DIR = srcdir("scripts")
ENV_DIR = srcdir("envs")
SRC_DIR = srcdir("workflow/scripts")
ENV_DIR = srcdir("workflow/envs")
DATA_DIR = config["data_dir"]
RESULTS_DIR = config["results_dir"]
DB_DIR = config["db_dir"]
......@@ -104,24 +104,24 @@ if 'taxonomy' in STEPS:
"workflow/steps/taxonomy.smk"
TARGETS += ["taxonomy_for_ont.done"]
# if 'analysis' in STEPS:
# include:
# "workflows/analysis.smk"
# # CD-HIT
# if "cdhit" in ANALYSIS_STEPS:
# TARGETS.append("cdhit_analysis.done")
# # Mappability
# if "mappability" in ANALYSIS_STEPS:
# TARGETS.append("mappability_index.done")
# # CRISPR
# if "crispr" in ANALYSIS_STEPS:
# TARGETS.append("crispr_analysis.done")
# # Plasmid prediction
# if "plasmids" in ANALYSIS_STEPS:
# TARGETS.append("plasmids_analysis.done")
# # AMR prediction
# if "amr" in ANALYSIS_STEPS:
# TARGETS.append("amr_analysis.done")
if 'analysis' in STEPS:
include:
"workflow/steps/analysis.smk"
# CD-HIT
if "cdhit" in ANALYSIS_STEPS:
TARGETS.append("cdhit_analysis.done")
# Mappability
if "mappability" in ANALYSIS_STEPS:
TARGETS.append("mappability_index.done")
# CRISPR
if "crispr" in ANALYSIS_STEPS:
TARGETS.append("crispr_analysis.done")
# Plasmid prediction
if "plasmids" in ANALYSIS_STEPS:
TARGETS.append("plasmids_analysis.done")
# AMR prediction
if "amr" in ANALYSIS_STEPS:
TARGETS.append("amr_analysis.done")
#else:
# raise Exception('You are not serious. No input data')
......
......@@ -2,7 +2,7 @@
# specify which rules to run
include:
'../rules/ANALYSIS_RULES'
'../rules/analysis.smk'
# Rule all for running the analysing partial gene counts in prodigal and unique gene counts with cd-hit on the proteins
rule CDHIT:
......
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