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usafsam
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mad_river_wf
SARS-CoV-2 analysis workflow, using Nextflow and bbtools
Apache License 2.0
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Retool workflow to add hMPXV
#33
fanninpm
opened
2 years ago
1
Remove `INTERLEAVE` step
#32
fanninpm
closed
2 years ago
0
Monkeypox
#31
fanninpm
opened
2 years ago
4
Add single reads mode
#30
fanninpm
closed
2 years ago
0
Upgrade nextclade to v2.0
#29
fanninpm
closed
2 years ago
0
Migrate to Nextclade v2.0
#28
fanninpm
closed
2 years ago
1
Support single-end reads
#27
fanninpm
closed
2 years ago
1
Add "run subtype" column to Performance file
#26
fanninpm
opened
2 years ago
0
Upgrade to Pangolin v4.0
#25
fanninpm
closed
2 years ago
0
Pangolin v4 upgrade aftermath
#24
fanninpm
closed
2 years ago
0
Generate higher coverage thresholds
#23
fanninpm
opened
2 years ago
0
Add new Midnight primers
#22
fanninpm
closed
2 years ago
0
Add VADR output to lineage excel file
#21
fanninpm
closed
2 years ago
0
Add new primers to Midnight set
#20
fanninpm
closed
2 years ago
5
Remove `.gz` from BAM outputs
#19
fanninpm
closed
2 years ago
0
Surface parameter for VADR container
#18
fanninpm
closed
2 years ago
1
Sort iVar consensus FASTA by sample name
#17
fanninpm
closed
2 years ago
4
Stop appending `.gz` to BAM outputs
#16
fanninpm
closed
2 years ago
1
Add Freyja to workflow
#15
fanninpm
opened
2 years ago
0
Switch to a BED file for primers/amplicons
#14
fanninpm
closed
2 years ago
5
Add VADR output to the lineage excel file.
#13
fanninpm
closed
2 years ago
0
Improve performance/lineage excel generation
#12
fanninpm
closed
2 years ago
0
Performance/Lineage excel file generation improvement
#11
fanninpm
closed
2 years ago
0
Generalize `SPIKE_GENE_COVERAGE` to cover all genes
#10
fanninpm
opened
2 years ago
2
Decrease pangolin stringency
#9
fanninpm
closed
2 years ago
2
Add VADR to workflow
#8
fanninpm
closed
2 years ago
0
Feed combined consensus FASTA to lineage tools
#7
fanninpm
closed
2 years ago
0
Decrease Pangolin stringency
#6
friesac
closed
2 years ago
0
Feed combined consensus FASTA to pangolin and nextclade
#5
fanninpm
closed
2 years ago
1
Make `ivar consensus` emit shorter FASTA header
#4
fanninpm
closed
2 years ago
2
Add VADR analysis to Mad River
#3
friesac
closed
2 years ago
2
Migrate to DSL2 and start modularizing
#2
fanninpm
closed
2 years ago
2
Updating readme file as example pull request
#1
friesac
closed
2 years ago
0