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ONT_pilot_gitlab
Commits
2e17bac2
Commit
2e17bac2
authored
4 years ago
by
Valentina Galata
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minor changes in Snakemake file
parent
98955ae9
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1 merge request
!76
Merge "cleanup" branch with "master" branch
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Snakefile
+19
-8
19 additions, 8 deletions
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2e17bac2
#
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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