Remove Illumina FASTQ suffixes from sample names — standardise_illumina_sample

Sample names in Mad4hatter outputs are the FASTQ file names up to the read (_R1/_R2), so they can still carry information added by the sequencer. This removes only those parts so the names match the manifest: the sample number (_S12) and, if present, the lane that follows it (_L001). A lane without a sample number is not removed, as Illumina always adds both. Anything else in the name is kept.

Usage

standardise_illumina_sample_name(sample_names, keep = character())

Arguments

sample_names: Character vector of sample names.
keep: Names to return unchanged.

Value

Character vector of standardised sample names.

Details

A name that ends in _S followed by digits but has no sequencer suffix (for example B1_S01) would lose that ending, so names listed in keep, usually the manifest sample names, are returned unchanged.

Examples

standardise_illumina_sample_name(c("sample1_S1_L001", "sample_A_S2"))
#> [1] "sample1"  "sample_A"

# Without `keep`, a name ending in _S<number> is trimmed
standardise_illumina_sample_name("B1_S01")
#> [1] "B1"
standardise_illumina_sample_name("B1_S01", keep = "B1_S01")
#> [1] "B1_S01"