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Valentina Galata authoredValentina Galata authored
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Snakefile 3.10 KiB
# File for running ONT analyses
##############################
# MODULES
import os
from tempfile import TemporaryDirectory
##############################
# CONFIG
# configfile:"config/CONFIG.yaml"
# Paths
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"]
# Steps
STEPS = config['steps']
ANALYSIS_STEPS = config["analysis_steps"]
# Input
BARCODES = config["barcodes"]
RUNS = [
config["runs"]["first"],
config["runs"]["second"],
# config["runs"]["third"]
]
SAMPLES = config["samples"]
BINNING_SAMPLES = config["binning_samples"]
# References
IGC_URI = config["igc"]["uri"]
HG38_URI = config["hg38"]["uri"]
REFERENCES = ["igc", "hg38"]
# Tools
ASSEMBLERS = config["assemblers"]
HYBRID_ASSEMBLER = config["hybrid_assembler"]
MAPPERS = ["bwa", "mmi"]
# default executable for snakmake
shell.executable("bash")
# working directory
workdir:
config["work_dir"]
# include rules for the workflows based on "steps" in the CONFIG.yaml file
# ONT analyses workflow
TARGETS = []
if 'assembly_annotation' in STEPS:
include:
"workflow/steps/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 'checkpoint_assembly_annotation' in STEPS:
include:
"workflow/steps/checkpoint_assembly_annotation.smk"
TARGETS += [
"assemble_and_coverage.done",
"annotate.done",
"basecall_merge_qc.done",
"basecall_merge_qc_NO_MOD.done",
"coverage_of_references.done",
"prodigal_gene_call.done",
"diamond_proteins.done",
"dummy_folders_created.done"
]
if 'mmseq' in STEPS:
include:
"workflow/steps/mmseq.smk"
TARGETS += [
"mmseq_comparison_for_ont.done"
]
if 'metaT' in STEPS:
include:
"workflow/steps/metat.smk"
TARGETS += ["metaT_mapping_for_ONT.done"]
if 'mapping' in STEPS:
include:
"workflow/steps/mapping.smk"
TARGETS += ["mapping_for_binning.done"]
if 'binning' in STEPS:
include:
"workflow/steps/binning.smk"
TARGETS += ["binning_for_ont.done"]
if 'taxonomy' in STEPS:
include:
"workflow/steps/taxonomy.smk"
TARGETS += ["taxonomy_for_ont.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')
# print("No input data provided")
rule all:
input:
TARGETS