ucsd-ccbb C-VIEW issues

ucsd-ccbb / C-VIEW

This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.

MIT License

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issues

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4.2.0

#158 AmandaBirmingham closed 1 year ago
0
sarscov2_v2_primers.bed

#157 antoine4ucsd opened 2 years ago
0
Update anaconda in install

#156 AmandaBirmingham opened 2 years ago
0
Add SamBamViz to pipeline

#155 niemasd opened 2 years ago
0
Major changes for 4.0.0

#154 AmandaBirmingham closed 2 years ago
0
Putative 3.9

#153 AmandaBirmingham closed 2 years ago
0
Support Genexus inputs

#152 AmandaBirmingham closed 2 years ago
0
Rearrange code structure

#151 AmandaBirmingham closed 2 years ago
0
Refactor misleading code in custom_gen_stats_multiqc

#150 AmandaBirmingham closed 2 years ago
0
Change to using slurm scheduler

#149 AmandaBirmingham closed 2 years ago
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Don't upload all fas for every lineage run

#148 AmandaBirmingham closed 2 years ago
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Incorporate use of metadata_cleared

#147 AmandaBirmingham closed 2 years ago
0
Test updates

#146 AmandaBirmingham closed 2 years ago
0
Support for Pangolin 4+

#145 AmandaBirmingham closed 2 years ago
1
Update pangolin to v4.0

#144 niemasd closed 2 years ago
1
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

#143 thomasbtf opened 2 years ago
0
Tree build removal, bug fixes

#142 AmandaBirmingham closed 2 years ago
0
[URGENT] Change samtools depth command

#141 niemasd closed 2 years ago
0
Updated links to samhead and pi_from_pileup

#140 niemasd closed 2 years ago
0
Putative 3.4.1

#139 AmandaBirmingham closed 3 years ago
0
update references to "covid_sequencing_analysis_pipeline" to "C-VIEW" in code and readme

#138 AmandaBirmingham closed 2 years ago
0
Putative 3.4

#137 AmandaBirmingham closed 3 years ago
0
Add bam S3 URLs to bjorn summary file

#136 AmandaBirmingham closed 3 years ago
0
Remove helix-specific processing from pipeline

#135 AmandaBirmingham opened 3 years ago
0
Reprocess recent SP runs without merging

#134 AmandaBirmingham opened 3 years ago
0
Putative 3.3

#133 AmandaBirmingham closed 3 years ago
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Include scripps-sequencing samples in bjorn summary

#132 AmandaBirmingham closed 3 years ago
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Use new submit_to_gisaid in populating ready for release column in bjorn summary

#131 AmandaBirmingham closed 3 years ago
0
Identify data transfer back-up person at SDSC

#130 AmandaBirmingham closed 2 years ago
0
Incorporate uDance into pipeline in place of de novo tree building

#129 AmandaBirmingham closed 2 years ago
1
Remove UCSD-specific code from pipeline for publication

#128 AmandaBirmingham opened 3 years ago
0
Build only stringent covid trees going forward

#127 AmandaBirmingham closed 2 years ago
0
Update pi_from_pileup to 1.0.3 and output entire pi_from_output TSV in addition to just pi metric

#126 niemasd closed 2 years ago
1
Update QC cutoffs for samples to include when building trees and run stringent only

#125 kmfisch closed 3 years ago
1
Fixed typo

#124 niemasd closed 3 years ago
0
Enable running pipeline on a single lane of a sequencing run

#123 AmandaBirmingham opened 3 years ago
0
Add an "auto" mode for merging in which need to merge is detected from sample names

#122 AmandaBirmingham opened 3 years ago
0
Add state abbreviation into virus name in bjorn summary

#121 AmandaBirmingham closed 3 years ago
2
Add fields to bjorn_summary file for easier Andersen lab processing

#120 AmandaBirmingham closed 3 years ago
0
Add support for miniARTIC primer set

#119 AmandaBirmingham closed 3 years ago
0
Add defensive checking of sample names

#118 AmandaBirmingham opened 3 years ago
2
Modify per-sample error log to exclude qualimap 255 errors (no reads) or don't run qualimap for those samples

#117 AmandaBirmingham closed 3 years ago
0
Produce sentinel files to indicate when pipeline has finished and whether had errors

#116 AmandaBirmingham opened 3 years ago
0
3.2.0

#115 AmandaBirmingham closed 3 years ago
0
Provide RTL-requested output files, add n metric check for failure condition

#114 AmandaBirmingham closed 3 years ago
0
Modify condition check for which samples are potentially eligible for GISAID deposition

#113 AmandaBirmingham closed 3 years ago
0
Provide RTL+CALM clinical- and wastewater-specific output files

#112 AmandaBirmingham closed 3 years ago
2
Support cumulative pipeline runs

#111 AmandaBirmingham closed 3 years ago
0
Add heterozygosity metrics, change default lineage/tree processing to per-sequencing-run

#110 AmandaBirmingham closed 3 years ago
0
Update samtools

#109 niemasd closed 3 years ago
1