From 98955ae9d162b3a28fef75a7c7bf40814ebbaa4a Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Tue, 9 Jun 2020 16:53:11 +0200
Subject: [PATCH] updated step analysis
---
Snakefile | 40 ++++++++++++++++++-------------------
workflow/steps/analysis.smk | 2 +-
2 files changed, 21 insertions(+), 21 deletions(-)
diff --git a/Snakefile b/Snakefile
index 9f3beaa..523b5f2 100755
--- a/Snakefile
+++ b/Snakefile
@@ -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')
diff --git a/workflow/steps/analysis.smk b/workflow/steps/analysis.smk
index 064d6ba..28b9d6f 100644
--- a/workflow/steps/analysis.smk
+++ b/workflow/steps/analysis.smk
@@ -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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