Open Valentin-Bio-zz opened 1 year ago
I'm transferring this issue to the nextstrain/ncov repository because the skip_diagnostics
configuration parameter is specific to the ncov workflow.
Hi @Valentin-Bio,
I did a dry run of the build using your config with:
nextstrain build . --configfile my-ncov-analyses/my_config.yaml --dry-run
I do not see the diagnostic
rule in the list of jobs, which means your config file should be properly set to skip the diagnostic rule.
Can you provide some more details to help us diagnose the issue?
results/everything/filtered_log.tsv
file to confirm the filter reasons?@Valentin-Bio Another possibility is that Snakemake is pulling in older intermediate files into your analysis that were generated before you updated the skip_diagnostics
setting in the config file. Older versions of Snakemake won't re-run the workflow based on parameter changes like this, so your workflow would appear to be running as you expected and still produce the wrong output.
One way around this issue is to force the workflow to run from scratch by adding the --forceall
argument to the snakemake
or nextstrain build .
command you're using.
Hello, I'm trying to run a next strain analysis using gisaid data. (export augur needed data from gisaid). After exporting the data (fasta and metadata files). I made my own configuration file (attaching here in txt format but it is in iml on my computer). my_config.txt
The analysis is removing all my samples (7 samples actually) because they fails on the diagnostic