Snakemake/Snake_biom at master · Aryunaa/Snakemake · GitHub

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DADA_d = "dada"
Dbiom= DADA_d + "/biom_out"


rule barplots:
	input:	DADA_d + "/table.qza",
		DADA_d + "/taxonomy.qza"

	output:
		DADA_d + "/barplots.qzv"
	shell:
		"qiime taxa barplot --i-table {input[0]} --i-taxonomy {input[1]} --o-visualization {output} --m-metadata-file metadata > {log}"

#барплоты не вышли - там какого-то файла не хватает, поищи metadata!

"""
rule convert:
	input:
		Dbiom + "/feature-table_meta.biom"
	output:
		Dbiom + "/feature-table_meta.txt"
	shell:
		"biom convert -i {input} -o {output} --to-tsv --table-type='OTU table' --header-key taxonomy"

rule sed_and_add_metadata:
	input:
		DADA_d + "/biom_out/feature-table.biom",
		DADA_d + "/biom_out/taxonomy.tsv"
	output:
		Dbiom + "/feature-table_meta.biom",
		Dbiom + "/sed_taxonomy.tsv"
	log:
		"logs/add_metadata.log"
	shell:
		y

		sed '1s/.*/#OTU ID\ttaxonomy\tConfidence/' {input[1]} > {output[1]}
		biom add-metadata -i {input[0]} -o {output[0]} --observation-metadata-fp {output[1]} --sc-separated taxonomy
		y


rule export_table_i_taxonomy:
	input:
		DADA_d + "/table.qza",
		DADA_d + "/taxonomy.qza"
	output:
		directory(Dbiom)
	log:
		"logs/export_table.log"
	shell:


		qiime tools export --input-path {input[0]} --output-path {output} > {log}
		qiime tools export --input-path {input[1]} --output-path {output} > {log}


rule biom:
	input:
		DADA_d + "/table.qza"
	output:
		DADA_d + "/table_4050.qza"

	log:
		"logs/export_taxonomy.log"

	shell:
		"qiime feature-table rarefy --i-table {input} --p-sampling-depth 4050 --o-rarefied-table {output} > {log}"

"""