Commit a8729799 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

count catalogue

parent da39f1fb
......@@ -95,10 +95,13 @@ rule metaspades:
"--min-length {params.min_len} "
def contigs_input(wildcards):
if config["ASSEMBLER"] == "megahit":
return ["work/megahit/{wildcards.sample}/{wildcards.sample}.contigs.fa".format(wildcards=wildcards)]
elif config["ASSEMBLER"] == "metaspades":
return ["work/metaSPADES/{wildcards.sample}/{wildcards.sample}.contigs.fasta".format(wildcards=wildcards)]
if wildcards.sample == "catalogue":
return ["work/cdhit/catalogue.ffn"]
else :
if config["ASSEMBLER"] == "megahit":
return ["work/megahit/{wildcards.sample}/{wildcards.sample}.contigs.fa".format(wildcards=wildcards)]
elif config["ASSEMBLER"] == "metaspades":
return ["work/metaSPADES/{wildcards.sample}/{wildcards.sample}.contigs.fasta".format(wildcards=wildcards)]
def contigsExpand_input(wildcards):
if config["ASSEMBLER"] == "megahit":
......
......@@ -11,12 +11,13 @@ rule all:
"report/quast_coassembly/report.html",
expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
"report/contigs_coassembly-taxNames.tsv",
expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
expand("report/count-gene-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
"report/genes_coassembly-taxNames.tsv",
"report/diamond_nr_coassembly.tsv",
"work/prokka/coassembly_prokka.tsv",
"work/interproscan/coassembly.faa.tsv",
"work/cdhit/catalogue.ffn",
expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]),
include: "../workflow_metagenomics/quality.smk"
......
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