| merge_bulk_fastq_python {FLAMES} | R Documentation |
Merges all fastq files in the given folder into a single file.
merge_bulk_fastq_python(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)