Register scrnaseq run

  1. Get a nf-core/scrnaseq run going

  2. Register fastq

  3. Consider tech and bio samples

  4. Register h5ad

!nextflow run nf-core/scrnaseq -r 2.7.1 -profile docker,test -resume –outdir output

!lamin init --storage run-scrnaseq --name run-scrnaseq --schema bionty,wetlab

! using anonymous user (to identify, call: lamin login)

import lamindb as ln
import bionty as bt
import wetlab as wl
from pathlib import Path

→ connected lamindb: anonymous/run-scrnaseq

# The fastq files were staged during the workflow execution. We get them from the work directory
fastq_files = [f for f in Path('work').rglob('*.fastq.gz') if f.is_symlink()]

The fastq files look like:

FFFFFFFFFFFFFFFFFFFFFFFFFF

@A00111:245:HGKNTDMXX:1:1101:3893:1000 1:N:0:NGGAGATG

TTGCCTCTGCATATTGTTCCTGATTG

+

FFFFFFFFFFFFFFFFFFFFFFFFFF

@A00111:245:HGKNTDMXX:1:1101:3929:1000 1:N:0:NGGAGATG

GATGCTACACAGGCCTTCATTGCTTT

+