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Commit 2e17bac2 authored by Valentina Galata's avatar Valentina Galata
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minor changes in Snakemake file

parent 98955ae9
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1 merge request!76Merge "cleanup" branch with "master" branch
# File for running ONT analyses
# Pipeline
##############################
# MODULES
......@@ -7,7 +7,8 @@ from tempfile import TemporaryDirectory
##############################
# CONFIG
# configfile:"config/CONFIG.yaml"
# can be overwritten by using --configfile <path to config> when calling snakemake
configfile: "config/CONFIG.yaml"
# Paths
SRC_DIR = srcdir("workflow/scripts")
......@@ -45,12 +46,16 @@ shell.executable("bash")
# working directory
workdir:
config["work_dir"]
config["work_dir"]
# include rules for the workflows based on "steps" in the CONFIG.yaml file
# ONT analyses workflow
##############################
# TARGETS & RULES
# List of targets to be created
TARGETS = []
# Include rules and add targets based on the config file
# Assembly annotation
if 'assembly_annotation' in STEPS:
include:
"workflow/steps/assembly_annotation.smk"
......@@ -77,6 +82,7 @@ if 'checkpoint_assembly_annotation' in STEPS:
"dummy_folders_created.done"
]
# MMSEQ2
if 'mmseq' in STEPS:
include:
"workflow/steps/mmseq.smk"
......@@ -84,26 +90,31 @@ if 'mmseq' in STEPS:
"mmseq_comparison_for_ont.done"
]
# MetaT
if 'metaT' in STEPS:
include:
"workflow/steps/metat.smk"
TARGETS += ["metaT_mapping_for_ONT.done"]
# Mapping
if 'mapping' in STEPS:
include:
"workflow/steps/mapping.smk"
TARGETS += ["mapping_for_binning.done"]
# Binning
if 'binning' in STEPS:
include:
"workflow/steps/binning.smk"
TARGETS += ["binning_for_ont.done"]
# Taxonomy
if 'taxonomy' in STEPS:
include:
"workflow/steps/taxonomy.smk"
TARGETS += ["taxonomy_for_ont.done"]
# Analysis
if 'analysis' in STEPS:
include:
"workflow/steps/analysis.smk"
......@@ -123,9 +134,9 @@ if 'analysis' in STEPS:
if "amr" in ANALYSIS_STEPS:
TARGETS.append("amr_analysis.done")
#else:
# raise Exception('You are not serious. No input data')
# print("No input data provided")
# No targets
if len(TARGETS) == 0:
raise Exception('You are not serious. Nothing to be done? Really?')
rule all:
input:
......
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