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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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Add --logfile switch to wrapper.py so logging information can be routed to a file instead of stdout.
#87
wshands
closed
7 years ago
2
Release 3.3.0
#86
jvivian
closed
7 years ago
0
Use samtools to sort (resolves #84)
#85
jvivian
closed
7 years ago
0
Use samtools to sort instead of STAR
#84
jvivian
closed
7 years ago
0
Update STAR to 2.5.3a
#83
jvivian
closed
7 years ago
1
Investigate newest STAR version
#82
jvivian
closed
7 years ago
1
Fix handling for output-dir as file URL
#81
jvivian
closed
7 years ago
0
Fix None bug for ids_to_delete
#80
jvivian
closed
7 years ago
0
wrapper.py should return non zero status on failure of pipeline
#79
wshands
closed
7 years ago
1
OSError: [Errno 2] No such file or directory from STAR
#78
wshands
closed
7 years ago
1
Add restart capability (resolves #76)
#77
jvivian
closed
7 years ago
1
Amend context manager to allow for restart
#76
jvivian
closed
7 years ago
0
Subprocess check_call Error if no logging option provided
#75
rcurrie
closed
7 years ago
2
Make wiki
#74
jvivian
closed
7 years ago
0
Fix bug when running single-end data (resolves #72)
#73
jvivian
closed
7 years ago
0
Error when running single end read data using Docker
#72
wshands
closed
7 years ago
1
Update toil-lib==1.1.6 (resolves #70)
#71
jvivian
closed
7 years ago
0
Update toil-lib==1.1.6
#70
jvivian
closed
7 years ago
0
Delete intermediates (resolves #67)
#69
jvivian
closed
7 years ago
0
Document Toil log and work mount requirement for docker run command
#68
wshands
closed
7 years ago
3
Delete intermediate files from jobStore
#67
jvivian
closed
7 years ago
0
Run DESeq2 Time Experiment
#66
jvivian
closed
7 years ago
1
Update tag for Docker image for RNA Seq 3.2.1 release
#65
wshands
closed
7 years ago
1
Update version tag for Dockstore and Quay.io
#64
wshands
closed
7 years ago
0
Update tag from 3.1.3 to 3.2.0-1
#63
wshands
closed
7 years ago
1
Release 3.2.x
#62
jvivian
closed
7 years ago
2
Add splice junction file from STAR to output (resolves #54)
#61
jvivian
closed
7 years ago
0
Update tag 3.1.3 (resolves #59)
#60
wshands
closed
7 years ago
2
Create release 3.1.3 for production
#59
wshands
closed
7 years ago
0
Add support for output file naming (resolves #57)
#58
wshands
closed
7 years ago
5
Add new argument to wrapper for output file basename
#57
wshands
closed
7 years ago
0
added code to provide output file basename
#56
tboser
closed
7 years ago
3
Evaluate expression differences with new GENCODE
#55
jvivian
closed
7 years ago
1
Modify pipeline to handle STAR SJ.out.tab
#54
jvivian
closed
7 years ago
0
Accept multiple fastqs as input (resolves #32)
#53
jvivian
closed
7 years ago
0
Analyze negative control experiments
#52
jvivian
closed
7 years ago
0
Add Toil context manager (resolves #50)
#51
jvivian
closed
7 years ago
0
Change start to Toil context manager
#50
jvivian
closed
7 years ago
0
Release 3.1
#49
jvivian
closed
7 years ago
0
Test newer STAR version for lockup issue
#48
jvivian
closed
7 years ago
7
Look into updating STAR version
#47
cket
closed
7 years ago
7
Properly concatenate gzipped fastq files
#46
cket
closed
7 years ago
1
Fix to CWL file for tar inputs
#45
wshands
closed
7 years ago
0
Remove promised reqs, fix disk values (resolves #41, resolves #42)
#44
jvivian
closed
7 years ago
0
Add entrypoint to generate inputs
#43
jvivian
closed
7 years ago
0
Adjust disk reqs based on 100 sample run
#42
jvivian
closed
7 years ago
0
Remove unnecessary PromisedRequirements
#41
jvivian
closed
7 years ago
0
Add disk to bamqc (resolves #38)
#40
jvivian
closed
7 years ago
0
Updating the version of workflow and toil
#39
briandoconnor
closed
7 years ago
0
Add disk req to run_bam_qc
#38
jvivian
closed
7 years ago
0
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