Fix: Replace biomformat with external biom in remove_bimera

The `biomformat` library is not well maintained and is only capable of
creating biom files of v1.0.0. This does not work properly when there is
only one column in the OTU table. Hence, we decided to use the external
`biom` command to create the table

micone/pipelines/templates/denoise_cluster/chimera_checking/remove_chimeras.R

@@ -3,27 +3,26 @@
 suppressWarnings(library(dada2))
 
 chimera.method <- "${chimera_method}"
-multithread <- ${ncpus}
+multithread <- as.integer("${ncpus}")
 
 # load table and convert to matrix
 seq.table.file <- "${seqtable_file}"
-seq.table <- read.csv(seq.table.file, sep="\\t", check.names=FALSE)
-rownames(seq.table) <- seq.table[,1]
-seq.table <- seq.table[ -c(1) ]
+seq.table <- read.csv(seq.table.file, sep = "\\t", check.names = FALSE)
+rownames(seq.table) <- seq.table[, 1]
+seq.table <- seq.table[-c(1)]
 seq.mat <- data.matrix(seq.table)
 mode(seq.mat) <- "integer"
 
 # chimera removal
-seq.table.nochim <- removeBimeraDenovo(t(seq.mat), method=chimera.method, multithread=multithread, verbose=TRUE)
+seq.table.nochim <- removeBimeraDenovo(t(seq.mat), method = chimera.method, multithread = multithread, verbose = TRUE)
 
 # Export sequences
 uniquesToFasta(
-   getUniques(seq.table.nochim),
-   fout="unhashed_rep_seqs.fasta",
-   ids=paste0("Seq", seq(length(getUniques(seq.table.nochim))))
+  getUniques(seq.table.nochim),
+  fout = "unhashed_rep_seqs.fasta",
+  ids = paste0("Seq", seq(length(getUniques(seq.table.nochim))))
 )
+write.table(t(seq.table.nochim), file = "seq_table_nochim.tsv", col.names = NA, sep = "\\t", quote = FALSE)
 
 # Export to biom
-library(biomformat)
-st.biom <- make_biom(t(seq.table.nochim))
-write_biom(st.biom, "unhashed_otu_table.biom")
+system("biom convert -i seq_table_nochim.tsv -o unhashed_otu_table.biom --to-hdf5")