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CGATOxford
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CGATPipelines
Collection of CGAT NGS Pipelines
MIT License
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Change time requested for job
#437
lucygarner
opened
1 year ago
2
resolvepackagenotfound
#436
miemonti
opened
5 years ago
1
Ah integrate cgat apps r deps
#435
AndreasHeger
closed
5 years ago
0
No transcript_info table with pipeline_genesets
#434
TomSmithCGAT
closed
6 years ago
2
Pipeline mapping fix
#433
jscaber
closed
6 years ago
0
Do not purge user modules during installation
#432
sebastian-luna-valero
closed
6 years ago
0
Update exome cancer
#431
BilyanaStoilova
closed
6 years ago
1
Update installation
#430
sebastian-luna-valero
closed
6 years ago
0
Copy environment to cluster jobs in SGE
#429
sebastian-luna-valero
closed
6 years ago
0
Ak firstbranch
#428
AlisonKennedy
closed
6 years ago
1
pipeline_peakcalling matplotlib.pyplot `.figure` error
#427
kevinrue
closed
6 years ago
2
fixes 424
#426
sebastian-luna-valero
closed
6 years ago
0
Added test for C/C++ compiler
#425
sebastian-luna-valero
closed
6 years ago
0
pipeline readqc fails to load FASTQC metrics of trimmed files?
#424
kevinrue
closed
6 years ago
18
fix cutadapt paired untrimmed command
#423
amayer21
closed
6 years ago
2
fix readqc pipeline.ini fastq_screen databases
#422
amayer21
closed
6 years ago
5
hard coded param in PipelinePeakcalling
#421
Acribbs
closed
6 years ago
0
added set(infiles) to loadReadCounts to avoid duplicating entries. Ha…
#420
nickilott
closed
6 years ago
2
pipeline_mapping.py uploads duplicated read counts when mergeReadCounts is not performed
#419
nickilott
closed
6 years ago
1
runFeatureCounts in PipelineRnaseq.py trys to create a temporary dire…
#418
nickilott
closed
6 years ago
10
Update snpEff from 4.1 to 4.3
#417
sebastian-luna-valero
closed
6 years ago
0
removed duplicate function
#416
Acribbs
closed
6 years ago
1
Ac chiptools
#415
Acribbs
closed
6 years ago
1
Bugfix https://github.com/CGATOxford/CGATPipelines/pull/412
#414
sebastian-luna-valero
closed
6 years ago
0
Typo
#413
kevinrue
closed
6 years ago
1
Increase priority of $HOME/.cgat ini file
#412
sebastian-luna-valero
closed
6 years ago
0
Copy environment to subprocess
#411
snsansom
closed
6 years ago
8
Changing the hierarchy of ini files
#410
sebastian-luna-valero
closed
6 years ago
0
Don't use conda 4.4
#409
sebastian-luna-valero
closed
6 years ago
0
Sns fix loading of gtf annotations
#408
snsansom
closed
6 years ago
1
Reference genome "*.fasta" in addition to ".fa"
#407
kevinrue
closed
6 years ago
2
Add back explicit reporting of failed cluster jobs
#406
snsansom
closed
6 years ago
1
Have updated PARAMS for template so it now points to the new genesets…
#405
Acribbs
closed
6 years ago
0
Ac bamstats report
#404
Acribbs
closed
6 years ago
0
Clarify expected fastq name for input files
#403
sebastian-luna-valero
closed
6 years ago
1
Sns fix memory pipeline genesets
#402
snsansom
closed
6 years ago
4
make threads=1 instead of threads=10 for build_report in pipeline.ini
#401
sebastian-luna-valero
closed
6 years ago
0
replace annotation reference in template
#400
Acribbs
closed
6 years ago
1
Prevent pipelines from running when DRMAA is not available and --local is not specified
#399
sebastian-luna-valero
closed
6 years ago
2
Small change to avoid confuision when running featurecounts
#398
Acribbs
closed
6 years ago
1
fix import of PipelineExomeAncestry
#397
BilyanaStoilova
closed
6 years ago
1
delay csvdb load tasks by a random offset to avoid database lock issues
#396
kevinrue
opened
6 years ago
5
changed way bam files are imported because the regex was incorrect wh…
#395
Acribbs
closed
6 years ago
2
bamstats report
#394
Acribbs
closed
6 years ago
1
bugfix cluster_queue in SGE with queue='' as new default
#393
sebastian-luna-valero
closed
6 years ago
8
update runGsea task in pipeline_enrichment
#392
sebastian-luna-valero
closed
6 years ago
0
Rename output for trim_galore
#391
sebastian-luna-valero
closed
6 years ago
0
Allow use of external pipelines with Control.py
#390
antoniojbt
closed
6 years ago
10
Update multiqc to version 1.4
#389
sebastian-luna-valero
closed
6 years ago
0
fastq naming convention
#388
sebastian-luna-valero
closed
6 years ago
5
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