issues
search
BimberLab
/
nimble
nimble — execute lightweight, flexible alignments on arbitrary reference libraries
MIT License
1
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Bump requests from 2.25.1 to 2.32.2
#70
dependabot[bot]
closed
2 months ago
0
Bump urllib3 from 1.26.5 to 1.26.19
#69
dependabot[bot]
closed
2 months ago
0
Bump idna from 2.10 to 3.7
#68
dependabot[bot]
opened
2 months ago
0
Bump zipp from 3.18.1 to 3.19.1
#67
dependabot[bot]
opened
2 months ago
0
Bump certifi from 2023.7.22 to 2024.7.4
#66
dependabot[bot]
closed
2 months ago
0
Suggestions for nimble debug/QC report
#65
bbimber
opened
2 months ago
1
Add validation to BAM/FASTQ input
#64
bbimber
opened
7 months ago
0
Re-enable --debug
#63
hextraza
opened
10 months ago
0
Fastq.gz not parsing appropriately
#62
hextraza
closed
9 months ago
4
Align should work with files instead of only paths
#61
hextraza
opened
10 months ago
0
Bump certifi from 2020.12.5 to 2023.7.22
#60
dependabot[bot]
closed
2 months ago
0
Bump requests from 2.25.1 to 2.31.0
#59
dependabot[bot]
closed
2 months ago
1
Update docker action versions
#58
bbimber
closed
1 year ago
0
Check exit code when running nimble aligner
#57
bbimber
closed
1 year ago
0
Bump certifi from 2020.12.5 to 2022.12.7
#56
dependabot[bot]
closed
1 year ago
1
Ensure samtools sort call on the UR flag keeps paired-end reads together
#55
hextraza
closed
1 year ago
1
Move baseline from 0->20 in score filter
#54
hextraza
closed
2 years ago
0
Add strandedness filters to alignment pipeline
#53
hextraza
closed
1 year ago
1
Sort mult-ref allele hits so the string is deterministic
#52
bbimber
closed
2 years ago
0
Implement a reference-library level option for 'max-hits-to-report'
#51
bbimber
closed
2 years ago
0
Bump numpy from 1.19.4 to 1.22.0
#50
dependabot[bot]
closed
2 years ago
1
Ensure align-debug output contains columns for all information relevant to filtering and decisions
#49
bbimber
closed
2 years ago
0
Update nimble's I/O to always override outputs, rather than append
#48
bbimber
closed
2 years ago
0
Look into why gzip output seems broken
#47
bbimber
closed
1 year ago
0
Update Dockerfile
#46
bbimber
closed
2 years ago
0
Empty string as the feature name?
#45
bbimber
closed
2 years ago
0
Check if discard_nonzero_mismatch is still in use
#44
hextraza
closed
2 years ago
0
Fix duplicated columns in library generation
#43
hextraza
opened
2 years ago
0
Trim long contigs from input data
#42
hextraza
closed
2 years ago
0
Enforce lack of comma in reference names, and also group_on fields
#41
bbimber
closed
2 years ago
0
group_on, when the target field is null
#40
bbimber
closed
2 years ago
0
--align-debug flag
#39
hextraza
closed
2 years ago
0
Do extra read checking
#38
hextraza
closed
2 years ago
0
Handle odd UMIs
#37
hextraza
closed
2 years ago
1
Add more output to the debug log
#36
hextraza
closed
2 years ago
0
Add clean step to Dockerfile to reduce image size
#35
hextraza
closed
2 years ago
1
Don't sort .bam files in-place
#34
hextraza
closed
2 years ago
2
Move docker build to Arch Linux
#33
hextraza
closed
3 years ago
0
check file extensions to ensure correct usage
#32
hextraza
closed
2 years ago
1
align with no parameters panics instead of printing usage
#31
hextraza
closed
10 months ago
0
generate step should sanity check the input and fail more gracefully
#30
bbimber
opened
3 years ago
0
Why does CSV need to list sequence length?
#29
bbimber
closed
10 months ago
0
Set OPENBLAS threads to 1
#28
hextraza
closed
3 years ago
0
Fix Docker build for Actions
#27
hextraza
closed
3 years ago
0
Fasta+CSV case
#26
hextraza
closed
3 years ago
1
New workflow
#25
hextraza
closed
3 years ago
0
Option to save results as mtx file instead of TSV
#24
bbimber
closed
2 years ago
1
Allow nimble create to work using CSV input?
#23
bbimber
closed
3 years ago
1
Bump urllib3 from 1.26.2 to 1.26.5
#22
dependabot[bot]
closed
3 years ago
0
0.1.0 release
#21
hextraza
closed
3 years ago
0
Next