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Snakefile
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Snakefile
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"""
workflow Snakefile
Author: Patricia Agudelo-Romero
email : [email protected]
███████╗██╗ ██╗███████╗██████╗ ███████╗███████╗████████╗
██╔════╝██║ ██║██╔════╝██╔══██╗██╔════╝██╔════╝╚══██╔══╝
█████╗ ██║ ██║█████╗ ██████╔╝█████╗ ███████╗ ██║
██╔══╝ ╚██╗ ██╔╝██╔══╝ ██╔══██╗██╔══╝ ╚════██║ ██║
███████╗ ╚████╔╝ ███████╗██║ ██║███████╗███████║ ██║
╚══════╝ ╚═══╝ ╚══════╝╚═╝ ╚═╝╚══════╝╚══════╝ ╚═╝
"""
import os
DIR = os.getcwd()
configfile: "config/config.yaml"
SAMPLES, = glob_wildcards(os.path.join(config["input_DIR"],"{sample}_R1.fastq.gz"))
if config["sequencing"] == 'PE':
include: "SMK/01_raw_qc_PE.smk"
include: "SMK/02_trimming_adaptors_PE.smk"
include: "SMK/03_Host_removal_PE.smk"
include: "SMK/04_DeNovo_PE.smk"
elif config["sequencing"] == 'SE':
include: "SMK/01_raw_qc_SE.smk"
include: "SMK/02_trimming_adaptors_SE.smk"
include: "SMK/03_Host_removal_SE.smk"
include: "SMK/04_DeNovo_SE.smk"
else:
include: "SMK/01_raw_qc_Long.smk"
include: "SMK/02_trimming_adaptors_Long.smk"
include: "SMK/03_Host_removal_Long.smk"
include: "SMK/04_DeNovo_Long.smk"
include: "SMK/05_Cleaning_contigs.smk"
include: "SMK/06_Taxonomy_nt.smk"
include: "SMK/07_Taxonomy_aa.smk"
include: "SMK/08_Summary_Taxonomy.smk"
#if config["annotation"] == 'RASTt':
# include: "SMK/07_annotation_RASTt.smk"
#else:
# include: "SMK/07_annotation_Prokka.smk"
rule all:
input:
#rawQC
os.path.join(config["output_DIR"],"EVEREST/multiQC_rep/raw_qc_multiqc_report.html"),
#adaptorsQC
os.path.join(config["output_DIR"],"EVEREST/multiQC_rep/trim_adaptors_multiqc_report.html"),
#Host_removal
os.path.join(config["output_DIR"],"EVEREST/multiQC_rep/fastq_before_merge_multiqc_report.html"),
#DeNovo
# expand(os.path.join(config["output_DIR"], "EVEREST/SPADES/{sample}/scaffolds.fasta"), sample=SAMPLES),
expand(os.path.join(config["output_DIR"], "EVEREST/MMSEQ_eLinclust/{sample}_all_seqs.fasta"), sample=SAMPLES),
expand(os.path.join(config["output_DIR"], "EVEREST/MMSEQ_eLinclust/{sample}_cluster.tsv"), sample=SAMPLES),
expand(os.path.join(config["output_DIR"], "EVEREST/MMSEQ_eLinclust/{sample}_rep_seq.fasta"), sample=SAMPLES),
#Viral contings enrichment
expand(os.path.join(config["output_DIR"], "EVEREST/CHECKV/{sample}/viruses_rename.fna"), sample=SAMPLES),
#Classification
os.path.join(config["output_DIR"], "EVEREST/Summary/Summary_nt_mmseqs2.txt"),
os.path.join(config["output_DIR"], "EVEREST/Summary/Summary_aa_mmseqs2.txt"),
#Summaries
os.path.join(config["output_DIR"], "EVEREST/Summary/Summary_mmseqs2.txt"),