Pipeline error and input file questions

[epifaniarango]

I am trying to run the popsize module. However, I didn't create my vcf files with snpArcher, which is becoming quite challenging. I am running the software, and I get the following error: No rule to produce popsize (if you use input functions make sure that they don't raise unexpected exceptions). The vcf file is located in snpArcher/results/hs37d5/yoruba_raw.vcf.gz, and the sample.csv file is the following:
BioSample,refGenome,refPath
HGDP00920,hs37d5,/scratch/earang/snpArcher/workflow/modules/popsize/data/hs37d5.fna
HGDP00924,hs37d5,/scratch/earang/snpArcher/workflow/modules/popsize/data/hs37d5.fna
HGDP00925,hs37d5,/scratch/earang/snpArcher/workflow/modules/popsize/data/hs37d5.fna
HGDP00926,hs37d5,/scratch/earang/snpArcher/workflow/modules/popsize/data/hs37d5.fna

I am quite confused about the pipeline in general. I also couldn't find information about whether the data needs phasing (which I assume it does, as it is required by msmc2) or how to input population information for each sample.

Thanks in advance for your time

[tforest]

Hello!
Thanks for trying the pipeline, that is very useful feedback. Could you please provide the snakemake command that you used to execute the pipeline?
Can you also provide a more detailed error log?
For your msmc2 question, it will be treated as unphased by default. It's still a work in progress but It would be nice to deal with that.
Many thanks!