This repository contains test datasets and reference files that are used as minimal input files for testing of nextflow pipelines.
Test data for IntGenomicsLab/lrsinglecell, used by its test* profiles.
| File | Used by profile |
|---|---|
lrsinglecell/samplesheet/samplesheet_test.csv |
test, test_lrkallisto |
lrsinglecell/samplesheet/samplesheet_test_dna.csv |
test_dna |
lrsinglecell/samplesheet/samplesheet_test_mixed.csv |
test_mixed |
lrsinglecell/samplesheet/samplesheet_full.csv |
test_full (points to the full ENA runs) |
lrsinglecell/fastq/sub_ERR9958133.fastq.gz, sub_ERR9958134.fastq.gz |
test, test_lrkallisto |
lrsinglecell/fastq/sub_RPMI8402_DNA.fastq.gz |
test_dna, test_mixed |
lrsinglecell/fastq/sub_RPMI8402_cDNA.fastq.gz |
test_mixed |
lrsinglecell/reference/chr21.fa, chr21.gtf |
all small profiles |
Provenance:
sub_ERR9958133/4.fastq.gz: ~5000 reads subsampled (seqtk sample -s123) from ERR9958133/ERR9958134 of You et al. (2023), Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE, Genome Biology 24:66, doi:10.1186/s13059-023-02907-y.sub_RPMI8402_{DNA,cDNA}.fastq.gz: subsampled in-house 10x Multiome ONT data of the RPMI-8402 cell line.chr21.fa/chr21.gtf: GENCODE GRCh38 v40, filtered to chr21.samplesheet_full.csv: from U-BDS/test-datasets@8ca6f50.
Attribution: the data files were copied unchanged (byte-identical, see lrsinglecell/SHA256SUMS) from nf-core/test-datasets, branch scnanoseq, commit 3fc8e5a (MIT License, Copyright (c) 2018 nf-core; see lrsinglecell/LICENSE-nf-core-test-datasets). The samplesheet_test*.csv files were changed only to point their FASTQ URLs at this repository.
The pipeline's nf-test snapshots depend on these exact bytes: do not modify files in place (add new files instead), and do not track them with git LFS, since raw URLs of LFS files return pointers.