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BD2KGenomics
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toil-rnaseq
UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
Apache License 2.0
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rnaseq-cgl-pipeline.cwl outputs doc string is off by two char
#137
wshands
closed
6 years ago
0
Autoscaling: RNA-Seq wrapper script no concatenation
#136
wshands
closed
6 years ago
0
Fix promise error when downloading fastqs (resolves #134)
#135
jvivian
closed
6 years ago
1
Bug: Error when downloading fastqs from S3
#134
jvivian
closed
6 years ago
1
Update config with direct links to inputs (resolves #131)
#133
jvivian
closed
6 years ago
0
Add Hera, localize tools/utils, and DAG refactor
#132
jvivian
closed
6 years ago
0
Find free hosting for RNA-seq inputs
#131
jvivian
closed
6 years ago
0
Autoscaling:RNA-Seq Toil Docker Proof of concept
#130
wshands
closed
6 years ago
2
Autoscaling CGP: Test and debug RNA-seq Docker changes
#129
wshands
closed
6 years ago
1
FAIL output
#128
moeishihara
closed
6 years ago
1
Look into adding Sphinx docs
#127
jvivian
opened
6 years ago
3
Make / outsource logo
#126
jvivian
closed
6 years ago
0
Rewrite the DAG statically
#125
jvivian
closed
6 years ago
0
Fix pypi push (resolves #123)
#124
jvivian
closed
6 years ago
0
Fix Jenkins push to PyPi
#123
jvivian
closed
6 years ago
0
Add ability to generate inputs (resolves #121)
#122
jvivian
closed
6 years ago
0
Add entrypoint to generate pipeline inputs
#121
jvivian
closed
6 years ago
0
Localize tool versions
#120
jvivian
closed
6 years ago
0
Feeding own STAR parameters
#119
moeishihara
opened
6 years ago
0
Look into HiSat2
#118
jvivian
closed
6 years ago
1
Enable Kallisto only processing; addresses #116
#117
wshands
closed
6 years ago
4
Support for Kallisto only determining expression counts
#116
wshands
closed
6 years ago
0
Docker version locking up on stacker and openstack
#115
rcurrie
closed
6 years ago
18
Add bam support with tests, GDC support, and user input (resolves #106, resolves #109, resolves #43, resolves #113)
#114
jvivian
closed
7 years ago
0
Add tests for bam input
#113
jvivian
closed
7 years ago
0
Jenkins fails on Docker push
#112
jvivian
closed
7 years ago
1
Move non-workflow functions outside main .py (resolves #110)
#111
jvivian
closed
7 years ago
0
Move non-pipeline functions outside of main .py
#110
jvivian
closed
7 years ago
0
Add GDC Download Support
#109
jvivian
closed
7 years ago
0
Add Pizzly
#108
jvivian
closed
6 years ago
3
Add Hera
#107
jvivian
closed
6 years ago
2
Add BAM support
#106
jvivian
closed
7 years ago
0
add logDebug switch as default to wrapper.py
#105
wshands
closed
7 years ago
1
fix image version tag
#104
wshands
closed
7 years ago
2
Fix Dockerfile so that Quay.io can build Toil RNA-Seq image
#103
wshands
closed
7 years ago
1
fix image tag version in rnaseq-cgl-pipeline.cwl
#102
wshands
closed
7 years ago
0
Add autoscaling to Toil RNA-Seq
#101
wshands
closed
7 years ago
1
New release of Docker version of Toil RNA-Seq
#100
wshands
closed
7 years ago
1
push short Docker tag to repo instead of long tag
#99
wshands
closed
7 years ago
5
push Docker short tag instead of long tag
#98
wshands
closed
7 years ago
1
fix zcat bug by using cat for all concatenation
#97
wshands
closed
7 years ago
1
Remove single-end prefix from UUID
#96
jvivian
closed
7 years ago
0
Fix cat zcat bug in wrapper
#95
wshands
closed
7 years ago
1
Add concordance validation to tests
#94
jvivian
closed
4 years ago
1
Allow option for user input when generating config / manifest
#93
jvivian
closed
6 years ago
1
Issues/use sdist in dockerfile #91
#92
wshands
closed
7 years ago
2
Enable Dockerfile to use python sdist so release of toil-rnaseq also builds Dockerfile
#91
wshands
closed
7 years ago
1
use zcat instead of python gzip for much faster performance
#90
wshands
closed
7 years ago
0
Issues/79 fix add return code
#89
wshands
closed
7 years ago
0
use subprocess zcat instead of python gzip in wrapper.py to speed up pipeline
#88
wshands
closed
7 years ago
0
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