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CDCgov
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phoenix
🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
Apache License 2.0
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[BUG] - create_samplesheet.sh file is no longer available
#170
snallani-msdh
opened
1 month ago
1
[BUG] - Undocumented setting docker.userEmulation
#169
jfnjdoh
closed
1 month ago
14
[BUG] - tile of issue
#168
ghost
closed
2 months ago
1
Create flags to turn on/off modules
#153
slsevilla
closed
3 weeks ago
2
Refactor failed summary handling
#152
slsevilla
opened
3 months ago
1
Move params checks upstream to main.nf
#151
slsevilla
opened
3 months ago
0
handle flags in nextflow.config rather than in main/modules
#150
slsevilla
closed
3 weeks ago
2
Update ICA, Terra handling to remove launchdir from module
#149
slsevilla
closed
3 weeks ago
1
Refactor pipeline filtering, create params flags for tools
#148
slsevilla
closed
3 weeks ago
2
handle failed samples via filtering
#147
slsevilla
opened
3 months ago
0
v2.1.1 dev merge to main
#146
HAISeq
closed
3 months ago
0
V2.1.1 dev
#145
HAISeq
closed
3 months ago
0
failure on AMRfinder (core dump)
#144
SeanSierra-Patev
closed
3 months ago
21
[BUG] - AMRFinder failing with core dump error on Terra
#143
cimendes
closed
4 months ago
5
Phoenix 2.1.0 MultiQC
#142
AmyR05
closed
3 months ago
7
Update modules.config - missing ncbi
#141
jvhagey
closed
4 months ago
0
update changelog
#140
jvhagey
closed
4 months ago
0
Update CHANGELOG.md
#139
jvhagey
closed
4 months ago
0
remove unnecessary file
#138
jvhagey
closed
4 months ago
0
branch alignment
#137
jvhagey
closed
4 months ago
0
Update phoenix.nf
#136
jvhagey
closed
4 months ago
0
updating
#135
jvhagey
closed
4 months ago
0
branch alignment
#134
jvhagey
closed
5 months ago
0
V2.1.0 dev
#133
jvhagey
closed
5 months ago
0
SPAdes_Failure that points to empty single reads file in v2.0.2
#132
TK-DPH
closed
3 months ago
8
[BUG] - Assembler identification can sometimes fail for flye
#131
jfnjdoh
closed
5 months ago
3
MLST calling wrong scheme
#130
vascokarla
closed
4 months ago
7
[BUG] - Resume flag restarts pipeline at SPADES, even if pipeline has completed downstream steps
#129
slsevilla
opened
5 months ago
2
[New Feature Request] - Why don't fastp, quast, and potentially other tools make it to the multiqc report?
#128
jfnjdoh
closed
5 months ago
2
Griphin steps being failed while running
#127
shovanmoon
closed
7 months ago
8
Workflow execution completed unsuccessfully. Exit status 125
#126
Murujit
closed
7 months ago
4
Running on Terra fails with a pigz not found error
#125
cvaske-clear
closed
9 months ago
2
[BUG] - tile of issue
#124
ghost
closed
4 months ago
4
Create message/output when downstream and QC analysis is not complete or is interrupted due to taxa not assigned (taxa is not bacterial)
#123
MOREYCK
opened
9 months ago
1
Fairy final
#122
MzDiaz824
closed
9 months ago
0
Memory issue when running test install script
#121
ghost
closed
10 months ago
6
pigz error in PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK process on GCP VM
#120
kprus
opened
10 months ago
6
NCBI_Assembly_stats_20230504.txt clarification
#119
cimendes
closed
10 months ago
3
PROKKA step failed in HPC (v2.0.2)
#118
tkiryuti
closed
5 months ago
5
[BUG] - CHECK_MLST failure
#117
ewalde1
closed
10 months ago
4
V2.0.2
#116
jvhagey
closed
11 months ago
0
MLST db error
#115
AmyR05
closed
11 months ago
4
Issue with running Phoenix on Terra
#114
lindseyb1234
closed
11 months ago
3
[BUG] - fastANI exit status 139 Segementation fault
#113
fnindo
closed
11 months ago
5
v2.0.1
#112
jvhagey
closed
12 months ago
0
v2.0.0
#111
jvhagey
closed
12 months ago
2
Revert "Read pair comparison"
#109
MzDiaz824
closed
1 year ago
0
Read pair comparison
#108
MzDiaz824
closed
1 year ago
0
Rd pr compr
#107
MzDiaz824
closed
9 months ago
0
MLST_Check_error
#106
fnindo
closed
1 year ago
6
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