Non-functioning sample wildcard (pipeline can't establish samples from input files and won't run)

[leahkemp]

I derped with this one

For cohort runs, I recently changed the output file path of the vcf file for human_genomics_pipeline v2.1.0. This coincided with changing the input file path of the vcf file for vcf_annotation_pipeline v1.1.0, converting the file extension from .g.vcf to .vcf.

I didn't update this properly in the sample widcard section for vcf_annotation_pipeline (see line 17 of the Snakefile), therefore the wildcard can't establish the sample names from the input files (and pipeline won't run).

If you come across this issue and don't want to rerun the pipeline and/or use a different version, you can simply change the wildcard for cohort runs (at line 17 in the Snakefile):

From: SAMPLES, = glob_wildcards("../../human_genomics_pipeline/results/called/{sample}_raw_snps_indels.g.vcf")
To: SAMPLES, = glob_wildcards("../../human_genomics_pipeline/results/called/{sample}_raw_snps_indels.vcf")

But of course I'll fix in the code too :)

[leahkemp]

Fix for this issue will be included in the next release, fix merged into dev branch