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fmalmeida
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bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
https://bacannot.readthedocs.io/en/latest/
GNU General Public License v3.0
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Use ICEO for ICE prediction?
#73
fmalmeida
opened
1 year ago
0
FIX: antismash results can be empty
#72
fmalmeida
closed
1 year ago
0
Issue with Antismash
#71
fetyj
closed
1 year ago
10
module for generating circos plot for contigs
#70
fmalmeida
closed
1 year ago
9
Tools to use own docker image
#69
fmalmeida
closed
1 year ago
3
Custom database report file bugs
#68
lam-c
closed
1 year ago
13
Minor improvements for custom database annotation
#67
lam-c
closed
1 year ago
6
Report failed
#66
fetyj
closed
1 year ago
2
adding rule to intersect bed
#65
fmalmeida
closed
1 year ago
2
problem with ResFinder annotation "merge"
#64
fmalmeida
closed
1 year ago
0
62 islandpath failed when there is no cds in bakta annotated gbk file
#63
fmalmeida
closed
1 year ago
0
ISLANDPATH failed when there is no CDS in Bakta annotated gbk file
#62
rujinlong
closed
1 year ago
5
Pipeline update: v3.1.3
#61
fmalmeida
closed
1 year ago
0
update hmmer to working version with PGAP (#59)
#60
fmalmeida
closed
1 year ago
0
update hmmer to working version with PGAP
#59
fmalmeida
closed
1 year ago
0
Adding option for using `bakta`
#58
fmalmeida
closed
1 year ago
2
add tool: pharokka
#57
fmalmeida
opened
2 years ago
0
Fixing error when phigaro output was empty (#55)
#56
fmalmeida
closed
2 years ago
0
Fixing error when phigaro output was empty
#55
fmalmeida
closed
2 years ago
0
workflow unsuccessful
#54
fetyj
closed
2 years ago
19
52 database downloading
#53
fmalmeida
closed
2 years ago
0
Database downloading
#52
fetyj
closed
2 years ago
9
Pipeline remodelling. Issues 24, 31 and 36 (#44)
#51
fmalmeida
closed
2 years ago
1
add tool: integron finder 2.0
#50
fmalmeida
closed
1 year ago
7
addition of ncbi_protein annotation module
#49
fmalmeida
closed
2 years ago
2
Merge changes from `develop`
#48
fmalmeida
closed
2 years ago
1
add tool: f5c (methylation)
#47
fmalmeida
opened
2 years ago
0
provide a small dataset for quick code tests
#46
fmalmeida
closed
2 years ago
9
Refactor channel identifiers and process names
#45
abhi18av
closed
2 years ago
12
Pipeline remodelling. Issues 24, 31 and 36
#44
fmalmeida
closed
2 years ago
4
Split out the config profiles
#43
abhi18av
closed
2 years ago
5
correct typo
#42
fmalmeida
closed
2 years ago
0
also accept samplesheet in CSV/TSV
#41
fmalmeida
opened
2 years ago
0
Input samples given only via samplesheet
#40
fmalmeida
closed
2 years ago
0
Use of named outputs in processes
#39
abhi18av
closed
1 year ago
10
Change case of modules/workflows to distinguish them from parameters
#38
abhi18av
closed
2 years ago
13
Split the configuration into multiple profiles with a dedicated folder
#37
abhi18av
closed
2 years ago
3
re-think modules organization and structure
#36
fmalmeida
closed
2 years ago
15
diminish pipeline complexity: pass sample always with YAML
#35
fmalmeida
closed
2 years ago
6
changed how tags are used
#34
fmalmeida
closed
2 years ago
0
possibility to set a global resfinder species value for samples in YAML
#33
fmalmeida
closed
2 years ago
2
Error with amrfinder
#32
fetyj
closed
2 years ago
6
annotation using list of gene IDs
#31
fmalmeida
closed
2 years ago
5
add a sourmash module
#30
fmalmeida
opened
2 years ago
1
merge develop into master
#29
fmalmeida
closed
2 years ago
0
Improve AMR report with hAMRonization tool
#28
fmalmeida
opened
2 years ago
1
Resfinder not being added to shiny app
#27
fmalmeida
closed
2 years ago
2
Issue23
#26
fmalmeida
closed
2 years ago
1
Add antiSMASH and SequenceServer BLAST
#25
fmalmeida
closed
2 years ago
4
Is it possible to diminish the main docker image?
#24
fmalmeida
closed
2 years ago
0
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