Matthew J. Oldach

No problem, I'll just set it up manually this time. Thanks and happy holidays!

Hi @jafors thanks for getting back to me. I've tried your suggestion of pipe the output from `samtools mpileup` to `varscan pileup2snp` between rules and adding another rule to combine...

Thanks for the suggestion. I've tried the following but get an error: ``` rule mpilup: input: bam=lambda wildcards: getDeduppedBams(wildcards.sample), reference_genome=os.path.join(dirs_dict["REF_DIR"],config["REF_GENOME"]) output: expand(os.path.join(dirs_dict["CALLING_DIR"],config["CALLING_TOOL"],"{sample}_{contig}.mpileup.gz"), sample=sample_names, contig=["I","II","III","IV","V","X","MtDNA"]) log: expand(os.path.join(dirs_dict["LOG_DIR"],config["CALLING_TOOL"],"{sample}_{contig}_samtools_mpileup.log"), sample=sample_names, contig=["I","II","III","IV","V","X","MtDNA"]) params: extra=lambda...

`vim +341 Snakefile` takes me to: ``` rule mpilup: input: bam=lambda wildcards: getDeduppedBams(wildcards.sample), reference_genome=os.path.join(dirs_dict["REF_DIR"],config["REF_GENOME"]) output: expand(os.path.join(dirs_dict["CALLING_DIR"],config["CALLING_TOOL"],"{sample}_{contig}.mpileup.gz"), sample=sample_names, contig=["I","II","III","IV","V","X","MtDNA"]) log: expand(os.path.join(dirs_dict["LOG_DIR"],config["CALLING_TOOL"],"{sample}_{contig}_samtools_mpileup.log"), sample=sample_names, contig=["I","II","III","IV","V","X","MtDNA"]) params: extra=lambda wc: "-r {}".format(wc.contig) resources: mem =...

Hi @jafors thank you very much for you help. This works wonderfully. However, I've noticed that the output of these two rules creates downstream issues with another rule #167

I've used the verbose flag `-r` to get a more comprehensive log: ``` Building DAG of jobs... Creating conda environment https:/github.com/snakemake/snakemake-wrappers/raw/0.64.0/bio/fastqc/environment.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create...

`bcftools view` is giving the warning from the output of `samtools mpileup`/`varscan pileup2snp`: ``` def getDeduppedBamsIndex(sample): return(list(os.path.join(aligns_dict[sample],"{0}.sorted.dedupped.bam.bai".format(sample,pair)) for pair in [''])) rule mpilup: input: bam=lambda wildcards: getDeduppedBams(wildcards.sample), reference_genome=os.path.join(dirs_dict["REF_DIR"],config["REF_GENOME"]) output: os.path.join(dirs_dict["CALLING_DIR"],config["CALLING_TOOL"],"{sample}_{contig}.mpileup.gz"),...

Re: the error > unsupported pickle protocol: 3 > "Perhaps the person who created the files wasn’t aware of the fact that the default protocol for pickle in Python 3...

Hi Egor, I would appreciate that. You can contact me at `[email protected]` Best, Matthew

Hi @cjfields the response was a bit late so this has been taken care of - Coovar runs _the same_ for me and my colleagues. However, in the interim we've...