merge_bulk_fastq {FLAMES} | R Documentation |
Merges all fastq files in the given folder into a single file.
merge_bulk_fastq(fastq_dir, out_fastq)
fastq_dir |
Path to the folder containing fastq files to merge |
out_fastq |
file path to the fastq file which will be created to store all fastq entries. Overwrites existing files |
file path to the created merged fastq file 'out_fastq'
# download the fastq files to merge temp_path <- tempfile() bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE) file_url <- "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data" # download the required fastq files, and move them to new folder fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq1", paste(file_url, "fastq/sample1.fastq.gz", sep = "/")))]] fastq2 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq2", paste(file_url, "fastq/sample2.fastq.gz", sep = "/")))]] fastq_dir <- paste(temp_path, "fastq_dir", sep = "/") # the downloaded fastq files need to be in a directory to be merged together dir.create(fastq_dir) file.copy(c(fastq1, fastq2), fastq_dir) unlink(c(fastq1, fastq2)) # the original files can be deleted # merge the fastq files out_fastq <- paste0(temp_path, "/outfastq.fastq.gz") ## Not run: merge_bulk_fastq(fastq_dir, out_fastq) ## End(Not run)