Check file integrity with md5sum
Arguments
- run_accessions
Character vector of run accessions.
- fastqdir
Path to the directory where .fastq files will be stored. Default: results/01_FASTQ_files.
Value
A data frame with variables Run and Status with run accession and integrity status, respectively.
Examples
urls <- c(
"ftp.sra.ebi.ac.uk/vol1/fastq/SRR926/SRR926397/SRR926397_1.fastq.gz",
"ftp.sra.ebi.ac.uk/vol1/fastq/SRR926/SRR926397/SRR926397_2.fastq.gz"
)
sample_info <- data.frame(
BioSample = "SAMN01924555",
Experiment = "SRX245306",
Run = "SRR926397",
BioProject = "PRJNA190191", Instrument = "Illumina HiSeq 2000",
Layout = "PAIRED"
)
fastqdir <- tempdir()
d <- download_from_ena(
sample_info, urls = urls, fastqdir = fastqdir, method = "libcurl"
)
#> Downloading file ftp.sra.ebi.ac.uk/vol1/fastq/SRR926/SRR926397/SRR926397_1.fastq.gz
#> Downloading file ftp.sra.ebi.ac.uk/vol1/fastq/SRR926/SRR926397/SRR926397_2.fastq.gz
# Check MD5
run_accessions <- sample_info$Run
check_md5(run_accessions, fastqdir)
#> Run Status
#> 1 SRR926397 TRUE