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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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Scaffolds samplesheet nf module creation
#58
MzDiaz824
closed
1 year ago
0
Scaffolds samplesheet creator
#57
MzDiaz824
closed
1 year ago
0
remove spades references
#56
MzDiaz824
closed
1 year ago
0
add workflow steps and placeholder for scaffolds
#55
MzDiaz824
closed
1 year ago
0
add external scaffold workflow
#54
MzDiaz824
closed
1 year ago
0
amrfinder_update: command not found
#53
Siddra2021
closed
1 year ago
9
kraken2_best_hit.sh error
#52
mndoucette
closed
1 year ago
7
[Question] - Why are coverages calculated with assembled length instead median genome size of species?
#51
rpetit3
closed
1 year ago
2
Question: RAM usage
#50
jenniferlu717
closed
1 year ago
2
Missing output file(s) *_best_MASH_hits.txt
#49
wchen190
closed
1 year ago
4
amrfinder_update: command not found
#48
Siddra2021
closed
1 year ago
2
Failed at the "SPADES (Test_Sample)" step
#47
tkiryuti
closed
1 year ago
2
Install Error
#46
ekeller8
closed
1 year ago
11
Can Pipeline be run without Docker or Singularity?
#45
AdrianLimaG
closed
1 year ago
4
V1.0.0
#44
jvhagey
closed
1 year ago
0
Srst2 2
#43
nvlachos
closed
1 year ago
0
[New Feature Request] - emit fastq files and contig files
#42
erinyoung
closed
1 year ago
5
Missing hash.k2d file and "uncommitted changes"
#41
DrB-S
closed
1 year ago
3
Create jsons
#40
MzDiaz824
closed
1 year ago
0
Diaz cdc sge
#39
MzDiaz824
closed
2 years ago
0
cdcsge config
#38
MzDiaz824
closed
2 years ago
0
Update nextflow.config
#37
MzDiaz824
closed
2 years ago
0
Update sra_phoenix.nf
#36
MzDiaz824
closed
2 years ago
0
update sra wk
#35
MzDiaz824
closed
2 years ago
0
change kraken trmd and pipeline stats
#34
MzDiaz824
closed
2 years ago
0
remove old spades module call
#33
MzDiaz824
closed
2 years ago
0
add spades wf module
#32
MzDiaz824
closed
2 years ago
0
update renaming fastas
#31
MzDiaz824
closed
2 years ago
0
add spades handling
#30
MzDiaz824
closed
2 years ago
0
test up to amrfinder
#29
MzDiaz824
closed
2 years ago
0
change comment sra wf
#28
MzDiaz824
closed
2 years ago
0
update sra workflow external
#27
MzDiaz824
closed
2 years ago
0
Internal sra
#26
MzDiaz824
closed
2 years ago
0
internal phoenix workflow
#25
MzDiaz824
closed
2 years ago
0
internal sra workflow
#24
MzDiaz824
closed
2 years ago
0
create cdc internal sra workflow
#23
MzDiaz824
closed
2 years ago
0
add amrfinder run to sra workflow
#22
MzDiaz824
closed
2 years ago
0
Amrfinder workflow
#21
MzDiaz824
closed
2 years ago
0
add installed modules to workflows
#20
MzDiaz824
closed
2 years ago
0
add amrfinder run module
#19
MzDiaz824
closed
2 years ago
0
add nfcore amrfinder update
#18
MzDiaz824
closed
2 years ago
0
delete sratools modules nf core
#17
MzDiaz824
closed
2 years ago
0
remove sratools nf core module
#16
MzDiaz824
closed
2 years ago
0
remove sra input param
#15
MzDiaz824
closed
2 years ago
0
sra test samples
#14
MzDiaz824
closed
2 years ago
0
chmod py file permissions
#13
MzDiaz824
closed
2 years ago
0
Sra input mod
#12
MzDiaz824
closed
2 years ago
0
config includes sra params
#11
MzDiaz824
closed
2 years ago
0
update output folders
#10
MzDiaz824
closed
2 years ago
0
correct sra samplesheet maker
#9
MzDiaz824
closed
2 years ago
0
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