Modules: adding test dataset for testing the hificnv module

[chaochaowong]

I would like to add the following dataset for the hificnv moduel tesing: (1)/data/genomics/homo_sapiens/pacbio/bam/SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.bam, (2)/data/genomics/homo_sapiens/genome/GRCh38_chr22.fa, and (3) /data/genomics/homo_sapiens/pacbio/vcf/SCRI_KT5028_GRCh38_downsampled_on_chr22_pbmm2_snv_hiphased.vcf.gz alone with their index files. Those were made specifically for testing the hificnv module and future pb-cpg-tools module. The existing test datasets do not have sufficient reads across a chromosome to run hificnv. So I included the downsized, aligned (against GRCH38), and snv-phased (hiphased) bam with 1000 reads across chr22 to test hificnv and minor allele files yielded by deepvariants for this specific bam file.

[inemesb]

Thank you for this addition! Is it necessary to add a new reference genome, or could you use one that already exists in the test datasets? The one you added is quite big, if it works with a smaller one it might be better to align to e.g. 'genome.fasta'.

[inemesb]

Very nice descriptions!

[chaochaowong]

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.

[inemesb]

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

[chaochaowong]

@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.