Commit 3037636c authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

Standardisation format sortie table d'abondances

parent 19be03b3
......@@ -1118,6 +1118,11 @@ if "denoiser" in config["global"]:
shell: """
qiime tools export --input-path {input} --output-path `dirname {output}`/{wildcards.taxorank}
biom convert -i `dirname {output}`/{wildcards.taxorank}/feature-table.biom -o `dirname {output}`/{wildcards.taxorank}.tsv --to-tsv
# Remove first header line to match with regular TSV format
tail -n +2 `dirname {output}`/{wildcards.taxorank}.tsv > `dirname {output}`/{wildcards.taxorank}_temp.tsv
mv `dirname {output}`/{wildcards.taxorank}_temp.tsv `dirname {output}`/{wildcards.taxorank}.tsv
rm -r `dirname {output}`/{wildcards.taxorank}
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