Commit 7d94c2f8 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

contigs_input(wildcards)

parent 4dcb27bf
......@@ -93,3 +93,9 @@ rule metaspades:
"-i work/metaSPADES/{wildcards.reads}/contigs.fasta "
"-o {output.contigs} "
"--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)]
......@@ -8,6 +8,7 @@ rule all:
input:
"report/multiqc_report.html",
expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
"report/contigs_coassembly-taxNames.tsv",
include: "../workflow_metagenomics/quality.smk"
include: "../workflow_metagenomics/preprocess.smk"
......
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