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chanzuckerberg
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idseq-workflows
Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
31
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12
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add archive message
#193
rzlim08
closed
2 years ago
0
Add diamond extra args flag
#192
rzlim08
opened
2 years ago
0
Add user error for insufficient coverage
#191
rzlim08
opened
2 years ago
0
Add minimap2/diamond local steps
#190
rzlim08
closed
2 years ago
0
add stage io map
#189
morsecodist
closed
2 years ago
0
Fix input json string to run_sfn
#188
rzlim08
closed
2 years ago
0
Add SFN benchmark inputs
#187
rzlim08
closed
2 years ago
0
Fix test when using the 2021-01-22 version of the NT/NR
#186
rzlim08
closed
2 years ago
0
Changed default alignment index from 2020-04-20 to 2021-01-22
#185
rzlim08
closed
2 years ago
0
Add minimap2 to wdl
#184
rzlim08
opened
2 years ago
1
Change max reads to 50M
#183
rzlim08
closed
2 years ago
0
Reduce max input for CG from 75,000,000 to 25,000,000
#182
rzlim08
closed
2 years ago
0
Reduce max input of consensus genomes from 75,000,000 to 25,000,000
#181
rzlim08
closed
2 years ago
0
fix STAR known errors by printing error JSON
#180
morsecodist
closed
2 years ago
1
Pipeline continue downloading essential files at every run
#179
Samiah-Kanwar
closed
2 years ago
2
raise maxlength to 500bp for illumina
#178
rzlim08
closed
2 years ago
0
Unable to Fetch Some Archives
#177
Samiah-Kanwar
closed
2 years ago
2
Alignment resolve outputs
#176
rzlim08
closed
2 years ago
0
Minimap2 Resolve Outputs
#175
rzlim08
closed
2 years ago
0
Disable stderr print on error
#174
rzlim08
closed
2 years ago
0
Separate step and integration tests
#173
rzlim08
closed
2 years ago
0
replace python script with seqkit (Go)
#172
rzlim08
closed
2 years ago
1
Subsample testing data and convert end-to-end tests to step tests
#171
rzlim08
closed
2 years ago
0
Increment accession version
#170
rzlim08
closed
2 years ago
1
ignore picard failures
#169
morsecodist
closed
2 years ago
0
Fix Star Status
#168
rzlim08
closed
2 years ago
0
Fix STAR status upload
#167
rzlim08
closed
2 years ago
0
Relabel phylo heatmap color bar
#166
rzlim08
closed
2 years ago
0
Updated pyvcf reference to fix falsey bug
#165
rzlim08
closed
2 years ago
0
changed input parameters
#164
rzlim08
closed
2 years ago
0
Fix broken tests
#163
rzlim08
closed
2 years ago
1
ignore divergent iqtree error
#162
morsecodist
closed
2 years ago
0
Run-GenerateCoverageStats map error mitigation
#161
rzlim08
closed
2 years ago
1
output ska.variants.aln if no tree is produced
#160
morsecodist
closed
2 years ago
0
fix output gene file name
#159
rzlim08
closed
2 years ago
1
fix bug with reading back idseq clusters
#158
morsecodist
closed
2 years ago
0
force path to genome to standard name
#157
rzlim08
closed
2 years ago
0
fix issue with clusters in phylotree
#156
morsecodist
closed
2 years ago
0
[CH-153676] Add coverage breadth to coverage_viz_summary output
#155
j-x-han
closed
2 years ago
0
enhance csv security
#154
morsecodist
closed
2 years ago
0
remove another instance of TooDivergentError from phylo tree
#153
morsecodist
closed
2 years ago
0
handle spaces in cg sample names
#152
morsecodist
closed
2 years ago
3
add error logging to generate coverage stats
#151
morsecodist
closed
2 years ago
0
fix select_first for newick
#150
morsecodist
closed
2 years ago
0
Tweak phylo heatmap style
#149
jshoe
closed
2 years ago
0
Add names to newick
#148
morsecodist
closed
2 years ago
0
[CH-143966] Adjust phylo heatmap styling
#147
jshoe
closed
2 years ago
0
updates to phylotree-ng README prior to v0 launch
#146
katrinakalantar
closed
2 years ago
0
Fix input min/max length when using midnight primers
#145
rzlim08
closed
2 years ago
0
Handle windows line endings
#144
rzlim08
closed
2 years ago
0
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