Delete makeSequenceTable.R

workflow/script/makeSequenceTable.R

-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)