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Snakefile
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Snakefile
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include: "rules/making_sample_dataset.rules"
print()
rule assembly:
input:
qualimap_report = "report/multiqc_assembly/multiqc_report.html",
buble_plot_maxbin = expand("samples/{sample}/binning/maxbin/gc_cov_buble_test.svg", sample = list(read_naming.keys())),
kaiju_phylum = expand("samples/{sample}/binning/kaiju/report_phylum.txt", sample = list(read_naming.keys())),
#chekm_maxbin = expand("samples/{sample}/binning/maxbin/checkm_bacteria/storage/bin_stats.analyze.tsv", sample = list(read_naming.keys()))
rule databases_setup:
input:
"reference_databases/virulence/VF_db.faa",
"reference_databases/virulence/VF_db_mmseqsDB"
rule homology_search:
input:
expand("samples/{sample}/mmseq_search/virulence/VF_db/best_hits.m8", sample = list(read_naming.keys())),
"report/mmseq_search/virulence/VF_db/annotation.log",
expand("samples/{sample}/mmseq_search/resistance/CARD_protein_homolog_model/best_hits.m8", sample = list(read_naming.keys())),
"report/mmseq_search/resistance/CARD_protein_homolog_model/annotation.log",
rule anvio:
input:
expand("samples/{sample}/assembly/spades/large_contigs_edit.fasta", sample = list(read_naming.keys()))
#expand("samples/{sample}/anvio/contigs_db/contigs.db", sample = list(read_naming.keys())),
pipeline_path = workflow.basedir + '/'
multiqc_configfile = pipeline_path + "data/configuration_files/multiqc/config.yaml"
# general
include: "rules/logging.rules"
# read manipulation
include: "rules/read_manipulation/get_reads.rules"
include: "rules/read_manipulation/get_sras.rules"
# quality check
include: "rules/QC/multiqc.rules"
include: "rules/QC/qualimap.rules"
include: "rules/QC/quast.rules"
include: "rules/QC/fastqc.rules"
include: "rules/QC/trimmomatic.rules"
# metagenomic assembly
include: "rules/assembly_and_binning/quality_check.rules"
include: "rules/assembly_and_binning/prodigal.rules"
include: "rules/assembly_and_binning/bwa.rules"
include: "rules/assembly_and_binning/assembly.rules"
include: "rules/assembly_and_binning/binning.rules"
# database setup
include: "rules/databases/virulence/virulence.smk"
include: "rules/databases/resistance/CARD.smk"
include: "rules/databases/mmseqs2.smk"
# taxonomy abundance
include: "rules/taxonomy_abundance/motus2.rules"
include: "rules/protein_abundance/calculate_RPKM.rules"
# anvio
include: "rules/anvio/anvio.rules"