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NationalGenomicsInfrastructure
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ngi_pipeline
Code driving the production pipeline at SciLifeLab
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Updates for sarek 3.4.2
#412
aanil
closed
2 months ago
0
Update import with change introduced in py3.10
#411
aanil
closed
3 months ago
3
Changed re to recognize NGI-U FU-projects
#410
monikaBrandt
closed
9 months ago
0
SNIC -> NAISS
#409
ssjunnebo
closed
1 year ago
0
Revert "parse sample name from fastq file instead of sample directory"
#408
b97pla
closed
2 years ago
0
devel
#407
b97pla
closed
2 years ago
0
Stage
#406
b97pla
closed
2 years ago
0
parse sample name from fastq file instead of sample directory
#405
b97pla
closed
2 years ago
0
Batch sarek analyses
#404
b97pla
closed
2 years ago
2
Special samplesheet path for MiSeq
#403
chuan-wang
closed
2 years ago
0
Fix decoding and error handling for python3
#402
ssjunnebo
closed
2 years ago
1
Update req to keep supporting py2.7
#401
aanil
closed
3 years ago
0
Increased qc walltime from 1 day to 3 days
#400
ghost
closed
3 years ago
1
Port to python 3
#399
ssjunnebo
closed
3 years ago
3
Remove more unused code and fix/add tests
#398
ssjunnebo
closed
3 years ago
4
Remove unused scripts and options
#397
ssjunnebo
closed
3 years ago
2
Increase request timeout to tide over slow charon conn
#396
aanil
closed
4 years ago
0
Bio 1876 adapt to nf core sarek rb
#395
b97pla
closed
4 years ago
2
add PR label enforcer
#394
ssjunnebo
closed
4 years ago
0
Added yaml loader type to stop display of warning message
#393
aanil
closed
4 years ago
0
improve fetching of analysis pipeline and reference from charon
#392
b97pla
closed
4 years ago
1
Fix path to bamqc results
#391
b97pla
closed
5 years ago
0
remove barcode from sample number logic
#390
b97pla
closed
5 years ago
0
continue updating charon status even if a sample raises exception
#389
b97pla
closed
5 years ago
1
Feature/sarek folder structure
#388
b97pla
closed
5 years ago
0
do cleanup of work directory after successful analysis
#387
b97pla
closed
5 years ago
3
Feature/sarek result parse
#386
b97pla
closed
5 years ago
0
LOG.warn -> LOG.warning
#385
matrulda
closed
5 years ago
13
exclude index files from sarek analysis
#384
b97pla
closed
6 years ago
0
determine libprep based on sample number, project id, sample name and…
#383
b97pla
closed
6 years ago
0
small renaming
#382
senthil10
closed
6 years ago
0
Sarek integration
#381
b97pla
closed
6 years ago
4
Create MD5 for fastq if required
#380
senthil10
closed
6 years ago
1
added documentation of the MD5-files
#379
b97pla
closed
6 years ago
2
filter out index files from analyses
#378
b97pla
closed
6 years ago
2
If this is a joke about how Swedes pronounce "w"
#377
mariogiov
opened
6 years ago
0
Updated acknowledgement text
#376
parlundin
closed
6 years ago
4
Feature/test with travis
#375
b97pla
closed
6 years ago
2
Non-existant variable referenced
#374
b97pla
opened
6 years ago
0
added sample name to md5 check
#373
Hammarn
closed
6 years ago
0
Allow index file to be passed to QC step
#372
Hammarn
closed
6 years ago
2
update bam2fastq.sh using latest libs
#371
szilvajuhos
opened
7 years ago
0
version bump
#370
vezzi
closed
7 years ago
0
Added static genotype concordance files to ngi_pipeline
#369
sylvinite
closed
7 years ago
0
Travis & Acknowledgements
#368
sylvinite
closed
7 years ago
0
Added acknowledgments file for easier citation
#367
sylvinite
closed
7 years ago
0
FRESH --> STALE upon FC organisation
#366
vezzi
closed
7 years ago
5
Added check for division by 0
#365
parlundin
closed
7 years ago
1
For GATK jarfile reliant scripts, set $GATK_HOME as default
#364
sylvinite
opened
7 years ago
0
Fixed gt_concordance bash collision on irma
#363
sylvinite
closed
7 years ago
0
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