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22 Open 105 Closed
22 Open 105 Closed
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Issues list

sarscov2_v2_primers.bed
#157 opened Aug 23, 2022 by antoine4ucsd
Update anaconda in install someday
#156 opened Aug 19, 2022 by AmandaBirmingham
Add SamBamViz to pipeline
#155 opened Jun 15, 2022 by niemasd
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly
#143 opened Mar 7, 2022 by thomasbtf
Remove helix-specific processing from pipeline someday
#135 opened Sep 9, 2021 by AmandaBirmingham
Reprocess recent SP runs without merging now pipeline run stakeholder request
#134 opened Sep 9, 2021 by AmandaBirmingham
Remove UCSD-specific code from pipeline for publication someday stakeholder request
#128 opened Aug 26, 2021 by AmandaBirmingham
Enable running pipeline on a single lane of a sequencing run someday
#123 opened Aug 16, 2021 by AmandaBirmingham
Add an "auto" mode for merging in which need to merge is detected from sample names someday
#122 opened Aug 16, 2021 by AmandaBirmingham
Add defensive checking of sample names someday stakeholder request
#118 opened Aug 16, 2021 by AmandaBirmingham
2
Produce sentinel files to indicate when pipeline has finished and whether had errors someday stakeholder request
#116 opened Aug 16, 2021 by AmandaBirmingham
Gzip all plain-text files someday
#102 opened May 24, 2021 by niemasd
2
Update Minimap2 to 2.24 someday
#94 opened Apr 9, 2021 by niemasd
4
Update ViralMSA someday
#92 opened Apr 2, 2021 by niemasd
1
Need to change coverage QC to include parts of the UTRs stakeholder request to prioritize
#81 opened Mar 24, 2021 by niemasd
Update samtools someday stakeholder request
#72 opened Mar 24, 2021 by niemasd
2
Exclude consensus sequences with coverage_gte_10_reads <70% from Bjorn processing someday stakeholder request
#66 opened Mar 19, 2021 by AmandaBirmingham
Append Bjorn output csv and indels to full-summary file someday stakeholder request
#60 opened Mar 19, 2021 by kmfisch
3
Implement Bjorn for indel flagging with help from Andersen lab someday stakeholder request
#59 opened Mar 19, 2021 by kmfisch
2
Need a way to put manually-reviewed and approved sequences back into "pipeline" someday
#52 opened Mar 17, 2021 by AmandaBirmingham
Add thread input parameters where fine-control optimization needed someday
#43 opened Mar 12, 2021 by AmandaBirmingham
1
Switch EBS software install from using anaconda to using miniconda someday
#12 opened Feb 26, 2021 by AmandaBirmingham
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