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Modules: adding test dataset for testing the hificnv module #1763

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e43c119
Add test datasets for hificnv module testing
chaochaowong Oct 23, 2025
7219335
edit README.md to add description of test datasets added for hificnv
chaochaowong Oct 23, 2025
6d8278f
added pacbio/vcf file for the hificnv module testing
chaochaowong Oct 23, 2025
1a3c2a6
edited READE.md for the description of the vcf file made for the hifi…
chaochaowong Oct 23, 2025
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6 changes: 6 additions & 0 deletions README.md
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@inemesb inemesb Nov 4, 2025

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Very nice descriptions!

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@chaochaowong chaochaowong Nov 6, 2025

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Thank you so much for reviewing it. I really appreciate it.
The aligned-phased BAM and MAF VCF files span the entire chr22, so the FASTA file also covers the whole chromosome and is indeed large, as you mentioned. I might try using homo_sapiens/genome/genome.fasta (chr22:16,570,000–16,610,000) to limit reads in the region, but I’m not sure if it’s based on GRCh38. Do you know? I’ll continue working on it this weekend. Thanks again.

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@inemesb inemesb Nov 6, 2025

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Yes, I think so based on what I see: https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/README.md#reference-files

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@chaochaowong chaochaowong Nov 9, 2025 •
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@inemesb Thanks for reviewing! I found that the genomics/homo_sapiens/pacbio directory includes suitable genome3.fasta, BAM, and VCF files for the hificnv module I submitted. I wasn’t very familiar with nf-core’s test datasets before, but I’m getting the hang of it now. Since the hificnv no longer needs the test datasets I made, I will close this PR. Thank you again for your help.

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Expand Up @@ -388,6 +388,8 @@ The earth sciences folder contain subfolders for different data formats encounte
- genome3.fasta: Reference fasta based on chr19:45760000-45770300
- genome_motifs.txt: TF motifs used for cellranger-atac
- genome.NC_012920_1.gb: Contains mtDNA reference genome in Genbank format
- GRCh38_chr22.fasta: GRCh38 reference fasta based on chr22
- GRCh38_chr22.fasta.fai: index file for 'GRCh38_chr22.fasta'
- transcriptome.fasta: Reference transcriptome based on `genome.fasta`
- gff3: Encode GFF3 file downsampled based on reference position
- gtf: Encode GTF file downsampled based on reference position, `genome_minimal.gtf` is a minimal version containing only the standard fields
Expand Down Expand Up @@ -609,6 +611,8 @@ The earth sciences folder contain subfolders for different data formats encounte
- NA03697B2_downsampled.pbmm2.repeats.bai: associated index to NA03697B2_downsampled.pbmm2.repeats.bam
- NA037562_downsampled.pbmm2.repeats.bam: subsample of puretarget pacbio reads from the [public pacbio dataset](https://downloads.pacbcloud.com/public/dataset/PureTargetRE/Coriell/PBMM2-BAM-Input-For-IGV-And-TRGT/) aligned to genome3.fasta
- NA037562_downsampled.pbmm2.repeats.bai: associated index to NA037562_downsampled.pbmm2.repeats.bam
- SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.bam: AML cell line down-sized sample of 1000 pbmm2-aligned and snv-phased sorted reads scattered on chr22; made for testing 'hificnv' and 'pb-cpg-tools' modules.
- SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.bam.csi: index file of 'SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.bam'
- bed:
- alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed: first set of gene models generated by TAMA collapse
- alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed: first set of gene models generated by TAMA collapse
Expand All @@ -628,6 +632,8 @@ The earth sciences folder contain subfolders for different data formats encounte
- FAM_snvs_annotated_ranked.vcf.gz: VCF file from HG002, only with ch16 generated from deepvariant and GLnexus
- FAM.ped: ped file associated with HG002
- peddy.sites: peddy standard hg38 sites downsampled to only chr16
- SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.vcf.gz: VCF file associated with 'SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.bam'
- SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.vcf.gz.tbi: Index file associated 'SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.vcf.gz'

- popgen:
- plink_simulated.bed: case-control simulated variants dataset in PLINK binary format
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508,186 changes: 508,186 additions & 0 deletions data/genomics/homo_sapiens/genome/GRCh38_chr22.fasta
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1 change: 1 addition & 0 deletions data/genomics/homo_sapiens/genome/GRCh38_chr22.fasta.fai
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chr22 50818468 7 100 101
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Binary file added ...omo_sapiens/pacbio/bam/SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.bam.csi
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Binary file added ...homo_sapiens/pacbio/vcf/SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.vcf.gz
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Binary file added ..._sapiens/pacbio/vcf/SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.vcf.gz.tbi
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