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chanzuckerberg
/
idseq-workflows
Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
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succeed without phylo tree
#143
morsecodist
closed
3 years ago
0
Error while Running Test Example - Consensus Genome
#142
Samiah-Kanwar
closed
2 years ago
11
Push docker images to ghcr.io
#141
mlin
closed
3 years ago
0
fix wdl test general consensus genome
#140
rzlim08
closed
3 years ago
0
Replace RunStar in host filter
#139
rzlim08
closed
3 years ago
2
add new RealignConsensus step
#138
katrinakalantar
closed
3 years ago
0
add muscle consensus realignment step to CG pipeline
#137
katrinakalantar
closed
3 years ago
0
add s3_wd_uri input to phylotree-ng
#136
morsecodist
closed
3 years ago
0
Replace STAR in host filter wdl
#135
rzlim08
closed
3 years ago
0
truncate consensus genome inputs
#134
morsecodist
closed
2 years ago
0
Add option for primer set
#133
rzlim08
closed
3 years ago
1
re-enable threading in bowtie2
#132
morsecodist
closed
3 years ago
0
fix bug with NA values in ska.distances.tsv and add known user error for divergent samples
#131
katrinakalantar
closed
3 years ago
1
Test various medaka models
#130
rzlim08
closed
3 years ago
1
Upgrade vadr model to vadr-models-sarscov2-1.2-2.tar.gz
#129
morsecodist
closed
3 years ago
1
don't emit valid input files
#128
morsecodist
closed
3 years ago
0
short-read-mngs RunAssembly: contig length filter
#127
mlin
closed
3 years ago
0
fix to address missing sample issue
#126
katrinakalantar
closed
3 years ago
0
meaningless change to trigger auto benchmark
#125
katrinakalantar
closed
3 years ago
1
remove nr-refseq output
#124
morsecodist
closed
3 years ago
0
Phylo Tree
#123
morsecodist
closed
3 years ago
2
Update samtools parameters to improve indel calling
#122
katrinakalantar
closed
3 years ago
1
handle null output_log_file
#121
morsecodist
closed
3 years ago
0
switch to initial space safety
#120
morsecodist
closed
3 years ago
0
quote clusters csv
#119
morsecodist
closed
3 years ago
0
optimize github actions jobs to avoid redundant runs
#118
morsecodist
closed
3 years ago
3
remove nt.refseq output
#117
morsecodist
closed
3 years ago
1
Santitize inputs for safe CSVs
#116
morsecodist
closed
3 years ago
2
emit star logfile
#115
morsecodist
closed
3 years ago
1
fix batch waiting bug
#114
morsecodist
closed
3 years ago
0
remove redundant manual timeout
#113
morsecodist
closed
3 years ago
0
raise proper insufficient reads error
#112
morsecodist
closed
3 years ago
0
Test change
#111
jshoe
closed
3 years ago
0
Add MN908947.3.fa test file
#110
jshoe
closed
3 years ago
3
Toward a working phylotree-ng
#109
kislyuk
closed
3 years ago
0
Upgrade VADR to v1.2
#108
kislyuk
closed
3 years ago
2
fix reading ska tsv
#107
morsecodist
closed
3 years ago
1
Bump taxoniq to v0.6.0
#106
kislyuk
closed
3 years ago
1
Add 2bp wiggle room to ivar primer trimming for tailedseq protocol
#105
katrinakalantar
closed
3 years ago
1
PhyloTree-NG workflow skeleton
#104
kislyuk
closed
3 years ago
0
Call VADR only on SC2 samples
#103
kislyuk
closed
3 years ago
0
Use flake8 in lint
#102
kislyuk
closed
3 years ago
0
Emit legible error on missing accession id
#101
kislyuk
closed
3 years ago
0
Update README.md
#100
katrinakalantar
closed
3 years ago
0
CG: Make length filter optional
#99
kislyuk
closed
3 years ago
0
Find/replace references to idseq-database
#98
jshoe
closed
3 years ago
0
possible issue with INDEL calling by samtools
#97
danrlu
opened
3 years ago
2
reduce the nanopore workflow min_length parameter to accommodate ClearLabs samples in the interim
#96
katrinakalantar
closed
3 years ago
1
Migrate readme comments from #74
#95
jshoe
closed
3 years ago
0
update to catch vadr errors and associated unit tests
#94
katrinakalantar
closed
3 years ago
0
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