Comments (3)
You can find them in the CTMR uppmax project under
/projects/WGS/kaisa_projects/Brachyspira/513A_R*.fastq.gz
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@thorellk, can you provide me with a sample input file that is contaminated with PhiX that I can use as a test?
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Please double check that it works as you want it to @thorellk, otherwise open this up again.
I made it so that the Nextflow code prepends phix,
to the adapter=
argument to BBDuk. I think the code looks clean, and I hope it works well.
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Related Issues (20)
- Update flowchart for new 3.0 options
- Update citation/publish pipeline HOT 25
- The documentation for 3.0 is not automatically updated by sphinx HOT 4
- Update changelog HOT 1
- BACTpipe workflow completed without errors HOT 1
- Shovill-Sendsketch skipping HOT 31
- Limit MultiQC search options HOT 7
- Running with the latest stable nextflow version (20.10.0) does not work HOT 2
- The docs still makes references to database paths HOT 2
- Warn user if signalp is missing if prokka_gram is true HOT 9
- SHOVILL process running with default threads 8 HOT 1
- Add automated testing via Github workflows HOT 1
- shovill.log output as standard HOT 6
- Replace SendSketch with Kraken2 HOT 2
- Invalid process definition -- Unknown keyword 'stub' @ line 20, column 5 HOT 5
- Changelog 3.1 HOT 2
- Include config file for large raw files? HOT 11
- Prokka process gets mixed inputs HOT 5
- bioconda::prokka environment error HOT 1
- Prokka isn't running if Kraken fails
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