Commit 053aff9e authored by Midoux Cedric's avatar Midoux Cedric
Browse files

DADA2 biom

parent c16471f6
......@@ -14,7 +14,8 @@ rule makeSequenceTable:
output:
rds = "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta",
tsv = "work/dada/seqtab.tsv"
tsv = "work/dada/seqtab.tsv",
biom = "work/dada/dada.biom"
threads:
config["THREADS"]
script:
......
library(dada2)
library(biomformat)
dada_list <- lapply(snakemake@input, readRDS)
names(dada_list) <- lapply(snakemake@input, function(x){basename(tools::file_path_sans_ext(x))})
......@@ -11,3 +12,6 @@ saveRDS(seqtab.nochim, snakemake@output$rds)
uniquesToFasta(seqtab.nochim, snakemake@output$fasta)
write.table(t(seqtab.nochim), snakemake@output$tsv, sep = "\t", quote = FALSE)
biom <- make_biom(t(seqtab.nochim))
write_biom(biom, snakemake@output$biom)
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