🐚 Add feature: New batch file scripts for documentation
One for when spades was used for the assembly, one where coverage is calculated using bwa/kart/samtools and one that uses the built in autometa coverages option with paired-end data. The spades one has been tested and ran successfully on the KwanLab server. A second test is ongoing on the agrp server in SA with a different, much larger dataset.
Note: For autometa_bwa_kart.sh to work, bwa kart and samtools will need to be added to the autometa conda env set up.
If you are happy with the scripts, I can create a QuickStart guide much as I did for the nextflow workflow.
PR checklist
[ x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ x] Have you followed the pipeline conventions in the contribution docs
🐚 Add feature: New batch file scripts for documentation
One for when spades was used for the assembly, one where coverage is calculated using bwa/kart/samtools and one that uses the built in autometa coverages option with paired-end data. The spades one has been tested and ran successfully on the KwanLab server. A second test is ongoing on the agrp server in SA with a different, much larger dataset.
Note: For autometa_bwa_kart.sh to work, bwa kart and samtools will need to be added to the autometa conda env set up.
If you are happy with the scripts, I can create a QuickStart guide much as I did for the nextflow workflow.
PR checklist