Commit 9e76ea37 authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

Delete makeSequenceTable.R

parent c02aaa31
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))})
seqtab <- makeSequenceTable(dada_list, orderBy = "abundance")
seqtab.nochim <- removeBimeraDenovo(seqtab, method="consensus", multithread = snakemake@threads, verbose = TRUE)
saveRDS(seqtab.nochim, snakemake@output$rds)
uniquesToFasta(seqtab.nochim, snakemake@output$fasta, ids = getSequences(seqtab.nochim))
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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