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Midoux Cedric authored4ee40425
import os
configfile: "./config.json"
SAMPLES=config["SAMPLES"]
rule all:
input:
"report/multiqc_report.html",
expand("report/reads_{sample}-krona.html", sample=SAMPLES),
#expand("report/contigs_{sample}-krona.html", sample=SAMPLES),
#"report/quast_results/report.html",
#expand("work/megahit/{sample}/{sample}.contigs.fa", sample=SAMPLES),
"work/megahit/coassembly/coassembly.contigs.fa",
"report/quast_coassembly/report.html",
"work/FGS/coassembly_FGS.gff",
"report/diamond-NR_coassembly.tsv",
expand("report/count-contigs-{sample}-coassembly.tsv", sample=SAMPLES),
expand("report/count-genes_FGS-{sample}-coassembly.tsv", sample=SAMPLES),
"report/genes_coassembly-taxNames.tsv",
"report/contigs_coassembly-taxNames.tsv"#,
#"work/eggnog/coassembly-bact.emapper.hmm_hits"
include: "quality.smk"
include: "preprocess.smk"
include: "kaiju.smk"
include: "assembly.smk"
include: "annotation.smk"
include: "count.smk"