Demultiplex 3RAD sequence libraries and merge samples duplicated across and within plates.
nextflow run \
main.nf \
--raw_read_paths <RAW READS>
--i7_index_path <i7 INDEX PATH>
--barcode_dir <BARCODE DIR>
--outdir <OUTDIR>
raw_read_paths: Path to raw reads. Use wildcard expansion. For example "*{1,2}.fq.gz". i7_index_path: Path to i7 index file. See below for details. barcode_dir: Path to directory containing sample barcode file. See below for details. outdir: Path to directory for output files.
Should be a tab separated file with index sequence followed by ID. ID must have two parts. An index ID and a plate ID separated by a hyphen. The plate ID must match the first part of the sample barcode file name. Also see example file.
For example:
| CGATAGAG | iTru7_111_01-plate1 |
| TTCGTTGG | iTru7_111_02-plate1 |
| GACGAATG | iTru7_111_05-plate2 |
| CATGAGGA | iTru7_111_06-plate2 |
| CTTCGTTC | iTru7_111_11-plate3 |
| CCAATAGG | iTru7_111_12-plate3 |
Should be a tab separated file with a barcode sequence followed by an ID. Underscores may only be used for within plate, sample duplicates. The first part of the filename separated by a hyphen, must match the plate ID used in the i7 index file. Also see example file.
For example:
plate1-barcodes.tsv
| CCGAATG | CTAACGT | sampleA |
| CCGAATG | TCGGTACT | sampleB |
| CCGAATG | GATCGTTGT | sampleC |
| CCGAATG | AGCTACACTT | sampleC_2 |
plate2-barcodes.tsv
| CCGAATG | CTAACGT | sampleD_1 |
| CCGAATG | TCGGTACT | sampleD_2 |
| CCGAATG | GATCGTTGT | sampleE |
| CCGAATG | AGCTACACTT | sampleF |
plate3-barcodes.tsv
| CCGAATG | CTAACGT | sampleA |
| CCGAATG | TCGGTACT | sampleB |
| CCGAATG | GATCGTTGT | sampleC |
| CCGAATG | AGCTACACTT | sampleD |