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UCSC-Treehouse
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pipelines
Makefiles to run dockerized pipelines used in Treehouse on a single sample
Apache License 2.0
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pre-check for write permissions before processing (Treeshop)
#40
e-t-k
opened
11 months ago
0
Thops466 ercc
#39
e-t-k
closed
1 year ago
0
How to handle failed fusion runs?
#38
e-t-k
opened
1 year ago
1
Pipeline does not support expanded FASTQ files, only gzipped
#37
e-t-k
opened
1 year ago
0
Pipeline does not support single end
#36
e-t-k
opened
1 year ago
0
Merge old develop changes into ERCC branch
#35
e-t-k
closed
1 year ago
0
pizzly crashes when run directly from Makefile
#34
e-t-k
opened
5 years ago
0
docs update for fusion
#33
e-t-k
closed
5 years ago
0
Update fusion docker version
#32
e-t-k
opened
5 years ago
0
Fusion update: Fixes #17 and #24 - fusion-generated bams go into derived; standalone fusion option
#31
e-t-k
closed
5 years ago
0
Develop - fixes #28 and #29
#30
e-t-k
closed
5 years ago
0
Add pizzly docker to process Kallisto fusion.txt
#29
e-t-k
closed
5 years ago
2
prune counts.jf from jfkm output before download
#28
e-t-k
closed
5 years ago
0
Add JFKM Pipeline
#27
jpfeil
closed
5 years ago
0
Custom tweak for CCLE compute: no fusion / bam download
#26
e-t-k
opened
5 years ago
0
Add FLT3-ITD Pipeline
#25
jpfeil
opened
5 years ago
0
fusion-generated bams should also go into primary/derived
#24
e-t-k
closed
5 years ago
1
Security update: Store downloaded bams in primary instead of downstream
#23
e-t-k
closed
5 years ago
1
place derived bams in primary
#22
e-t-k
closed
5 years ago
1
Makefile: should crash when finding N>2 fastq files
#21
e-t-k
opened
5 years ago
0
Explore lite pipeline
#20
rcurrie
opened
5 years ago
4
fix source of input bam in the methods.json file for variant calling
#19
e-t-k
closed
5 years ago
2
Improve Treeshop's ability to recognize R1/R2 naming conventions
#18
klearned
opened
6 years ago
1
Add a flag to run only fusion
#17
e-t-k
closed
5 years ago
0
Use bam from umend for min-var call
#16
rcurrie
closed
6 years ago
4
Preserve the bam from umend and use it for min-var-call
#15
rcurrie
closed
6 years ago
0
Add experimental support for S3/CEPH and test on Jacob's files
#14
rcurrie
closed
5 years ago
9
Updates to documentation for initial setup
#13
ghost
closed
5 years ago
7
Updates to treeshop.md documentation
#12
ghost
closed
5 years ago
1
Develop
#11
rcurrie
closed
6 years ago
0
Develop
#10
rcurrie
closed
6 years ago
0
Develop
#9
rcurrie
closed
6 years ago
0
Support bam's as input to treeshop
#8
rcurrie
closed
6 years ago
5
Pull doc edits
#7
rcurrie
closed
6 years ago
0
Develop
#6
rcurrie
closed
6 years ago
0
Unable to communicate over ssh to greater then 6 machines
#5
rcurrie
closed
6 years ago
2
Major upgrade including variant, bug fixes, and better documentation
#4
rcurrie
closed
6 years ago
0
Output layout
#3
rcurrie
closed
6 years ago
0
Upgrade to 3.2.1 expression pipeline and add support for fusion pipeline
#2
rcurrie
closed
7 years ago
0
canonical transcripts, gene model, genomic coordinates
#1
cchng
closed
7 years ago
2