Commit ad1b7e72 authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

ANCOM and DESEq2 needs taxonomy firest

parent d13e00a8
Pipeline #23274 failed with stages
in 57 minutes and 4 seconds
......@@ -618,12 +618,13 @@ def format_all_rule():
all_input.append(getOutput("summarize_table", "plots/prevalence_abundance.html"))
all_input += expand(getOutput("taxorank_tables", "{taxorank}_table.tsv"), taxorank=["phylum", "class", "order", "family", "genus", "species"])
if "ancom" in config.keys():
all_input += expand(getOutput("ancom", "{taxorank}/volcano/index.html"), taxorank=["phylum", "class", "order", "family", "genus", "species", "asv"])
if "deseq2" in config.keys():
all_input.append(getOutput("deseq2/asv", config["deseq2"]["condition"]))
all_input += expand(getOutput("deseq2/{taxorank}", config["deseq2"]["condition"]), taxorank=["phylum", "class", "order", "family", "genus", "species"])
if "deseq2" in config.keys():
all_input.append(getOutput("deseq2/asv", config["deseq2"]["condition"]))
all_input += expand(getOutput("deseq2/{taxorank}", config["deseq2"]["condition"]), taxorank=["phylum", "class", "order", "family", "genus", "species"])
if "ancom" in config.keys():
all_input += expand(getOutput("ancom", "{taxorank}/volcano/index.html"), taxorank=["phylum", "class", "order", "family", "genus", "species", "asv"])
return all_input
......
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