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NorwegianVeterinaryInstitute
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Bifrost
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Added saga specific run track
#54
karinlag
closed
4 months ago
0
modifying nextflow command to use specific version
#53
karinlag
closed
1 year ago
0
Check: Possibility output DataTable to allow filtering assemblies (&evt. sequencing quality) by quality easily
#52
evezeyl
opened
1 year ago
0
Prokka removal
#51
karinlag
closed
2 years ago
0
Summer 2022 update
#50
karinlag
closed
2 years ago
0
202207 v2
#49
karinlag
closed
2 years ago
0
Improvement
#48
evezeyl
closed
2 years ago
1
Switch from SPAdes and pilon to Unicycler?
#47
hkaspersen
closed
2 years ago
2
Fixes Issue 45 with regards to reuse of database with multiple datasets.
#46
karinlag
closed
4 years ago
0
Fix specific genes so to allow reuse of database with multiple read sets
#45
karinlag
closed
4 years ago
0
Enables the use of locally downloaded databases
#44
karinlag
closed
4 years ago
1
Fix specific gene finding to allow outside downloading
#43
karinlag
closed
4 years ago
1
Add plasmidfinder as own analysis in config file
#42
hkaspersen
closed
2 years ago
1
Output from MLST is not tab separated
#41
hkaspersen
opened
4 years ago
0
Closing issue 38
#40
karinlag
closed
4 years ago
0
Bifrost 2.0
#39
ajkarloss
opened
4 years ago
1
Bifrost in Saga
#38
karinlag
closed
4 years ago
2
Pilon java heap space memory issue
#37
Thomieh73
closed
4 years ago
1
Change R1/R2 in the collate process
#36
karinlag
opened
5 years ago
0
no output from qc_track using normal config template
#35
evezeyl
opened
5 years ago
0
summary statistics
#34
evezeyl
opened
5 years ago
0
to reuse or not reuse spade corrected reads - that is the question...
#33
evezeyl
opened
5 years ago
1
pilon options? break contigs and local realignement
#32
evezeyl
opened
5 years ago
0
remove unused parameter from asm_annot_template.config
#31
evezeyl
opened
5 years ago
0
optional input corrected reads from spades?
#30
evezeyl
closed
2 years ago
3
bwamem PE mapping and into pilon
#29
evezeyl
opened
5 years ago
0
Finding Contaminants and Removing them
#28
ajkarloss
opened
5 years ago
2
Merging PhiX removal and quality/adapter removal/trimming into one step process
#27
karinlag
closed
2 years ago
0
Solving issue 25 re work directory
#26
karinlag
closed
5 years ago
0
Figure out how to save data on userwork instead of disk
#25
karinlag
closed
5 years ago
3
qc_track has link instead of copy as savemode
#24
karinlag
opened
5 years ago
0
Getting the permission stuff correct.
#23
karinlag
closed
5 years ago
0
Modifying runtrack to fix permissons problems
#22
karinlag
closed
5 years ago
0
Actually committing the python file necessary for filtering lengths,
#21
karinlag
closed
5 years ago
0
Correcting 19 in main repo, ensuring that permissons for work is in
#20
karinlag
closed
5 years ago
0
Change permissions on output directory
#19
karinlag
closed
5 years ago
0
Solves NVI BIFROST issue 15
#18
karinlag
closed
5 years ago
0
Solving iss 16 in NVI BIFROST repo
#17
karinlag
closed
5 years ago
0
Add remove short scaffolds to spades
#16
karinlag
closed
5 years ago
0
add possibility for --split-scaffolds to quast parameters in config file
#15
hkaspersen
closed
5 years ago
1
Add possibility to select genes of interest and get a multi-fasta file with these genes
#14
hkaspersen
opened
5 years ago
0
Add fastqc step after data pre-processing
#13
Girum12
opened
5 years ago
0
trimmomatic gives wrong log file
#12
Girum12
opened
5 years ago
0
multiqc locale
#11
snogu
closed
5 years ago
1
Fixing precmd, savemode and javaopts for pilon
#10
karinlag
closed
5 years ago
0
add --compliant to asm_annot pipeline default prokka config
#9
hkaspersen
opened
6 years ago
0
Fixing joins between files
#8
karinlag
closed
6 years ago
0
Fix queuesize
#7
karinlag
closed
6 years ago
0
v0.2.1
#6
karinlag
closed
6 years ago
0
Updating slurm.conf to set the maxForks and the default time
#5
karinlag
closed
6 years ago
0
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