David O'Connor

Python error when creating subdirectories

8

**Snakemake version** 7.3.8 **Describe the bug** This may be related to https://github.com/snakemake/snakemake/pull/1588 I need to run Snakemake within a Docker container. Workflows that used snakemake 5.29.0 work fine. When I...

Longitudinal sequencing from individuals with prolonged SARS-CoV-2 has some different attributes than spot sequencing of individual cases. Can the metadata standards be updated to handle longitudinal sampling? Some considerations: -...

Enhancement: add whitelist to pre-processing

2

Thanks for this very useful workflow. To reduce runtimes, can I suggest adding a 'whitelist' rule to preprocessing? This could reduce runtimes considerably in situations where the targets are limited...

Minimap2 --split-fasta?

1

### Description of the bug The workflow is failing at MINIMAP2_ALIGN with two errors: 1. Minimap2 can't process FASTA headers unless `--split-prefix` is specified 2. SAM sorting has the flag...

rdrp5?

1

Hi there, I began exploring serratus-lite to profile RNA viruses in wastewater datasets this week using the RNA Virus RdRP Search workflow described at: https://github.com/ababaian/serratus/wiki/Serratus-Lite When I looked at the...