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License: MIT License
This project forked from michellejlin/covid_swift_pipeline
License: MIT License
sponsor requests coverage info generated using samtools:
samtools depth -a -H <sorted.bam>
Please implement for the iupac_edit branch
Looks like we're outputting NA for mapped reads after mapping with bwa-mem. Possible to include count of mapped reads?
covid_swift_pipeline/modules.nf
Line 165 in 76b331e
(this is just for the iupac-edit branch)
Can we just have a single process to do the pileup and pipe into ivar since we're not really using the pileup output for anything else here?
covid_swift_pipeline/modules.nf
Line 2 in 10505bd
Why are concatentated fastqs being used at this step rather than paired R1/R2s?
Can we update to make the mapping paired-end aware?
covid_swift_pipeline/modules.nf
Line 165 in e5e8db8
This line results in an error if --NO_CLIPPING is enabled.
--NO_CLIPPING specified. Skipping primer clipping step...
Unknown method invocation `toUpperCase` on Boolean type
-- Check script '.nextflow/assets/greninger-lab/covid_swift_pipeline/main.nf' at line: 126 or see '.nextflow.log' file for more details
Line 126 in d8d8b05
Don't think we need to save these, right? @michellejlin
covid_swift_pipeline/modules.nf
Line 95 in d8d8b05
QIAGEN released boosters to improve coverage with Omicron: https://www.qiagen.com/us/resources/resourcedetail?id=d98e01ad-4c27-483a-b473-74dcd3d9cadf&lang=en
Need to add support for this in trimming step as a new option under --PRIMERS
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