Comments (2)
fmaguire
commented on June 20, 2024
Hi @thomasbtf,
Thanks for reaching out!
I submitted a PR with some modifications to the SIGNAL summary: IKIM-Essen/sars-cov-2-workflow-comparison@main...fmaguire:patch-1
PHA4GE has also gathered some information about bioinformatics resources for SARS-CoV-2 that may be useful to your efforts! https://github.com/pha4ge/pipeline-resources/blob/main/docs/bioinfo-solutions.md
from covid-19-signal.
jaleezyy
commented on June 20, 2024
Hi @thomasbtf,
Taking a look at @fmaguire's patch, I agree with his changes! I would propose the re-addition of iVar into the consensus and variant calling sections, given both are still supported with the latest version of SIGNAL, although FreeBayes is prioritized.
PR: IKIM-Essen/sars-cov-2-workflow-comparison@main...jaleezyy:patch-1
from covid-19-signal.
Related Issues (20)
- Add lineage assignments to summary table HOT 1
- Pangolin Update changes probability column to conflict breaking assign_lineages.py HOT 1
- Lineage Assignment Failure preventing postprocess HOT 1
- Switch remaining default output to freebayes vs iVar
- Primer Scheme Correction HOT 1
- Revisit output layout
- Add Continuous Integration tests and linting
- Fix containerization
- Convert rules for wrapped tools to official wrapper
- support for pangolin v3.0.1 HOT 2
- ValidationError: 'sample' is a required property HOT 2
- Incorporate scorpio calls into report
- Galaxy workflow?
- Support IonTorrent .bam input
- Cleanup
- RuleException in line 549 of: filepath/Snakefile: 'Params' object has no attribute 'unlabelled_output_dir' HOT 2
- Update npm nextclade to the proper nextclade_cli HOT 1
- gunzip silently fails when running get_data_dependencies.sh HOT 1
- Pipeline fails at run_lineage_assignment when trying to use Nextclade version 3.0.0 HOT 4
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