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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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'The termination flag is set, exiting' with docker version 'rnaseq-cgl-pipeline:3.2.1-1'
#187
zhenzhenyang-psu
opened
2 years ago
1
SELinux?
#186
aubreybailey
opened
3 years ago
1
fastqc failed with file not found
#185
genec1
closed
3 years ago
4
toil-rnaseq failure: 'Expando' object has no attribute 'ci_test'
#184
genec1
closed
3 years ago
2
Toil run dying on SRA fastq file
#183
genec1
closed
3 years ago
2
bd2k version incompatibility between toil-rnaseq and s3am
#182
genec1
opened
4 years ago
0
Unable to install -- python incompatabilities
#181
genec1
closed
4 years ago
2
Pin Toil version due to backwards compatibility Docker change
#180
jvivian-atreca
closed
4 years ago
0
Is there any options that could not run hera in config files?
#179
biosyf
closed
5 years ago
1
command not found
#178
cynthia143234
closed
5 years ago
4
quantification for stranded data
#177
yuankunzhu
opened
5 years ago
6
Update GDC container (resolves #175)
#176
jvivian
closed
5 years ago
0
Fix gdc-client container
#175
jvivian
closed
5 years ago
0
Investigate FASTP as a replacement for FastQC and CutAdapt
#174
jvivian
closed
4 years ago
1
AttributeError: 'Expando' object has no attribute 'bamqc'
#173
hmkim
closed
5 years ago
2
Should PAR locus on the Y chromosome be removed in RSEM pipeline?
#172
wangshun1121
opened
5 years ago
3
Add explanation to FAQ regarding default kallisto indices
#171
jvivian
opened
5 years ago
0
Where is transcriptome_hg38_gencodev23.fasta from?
#170
wangshun1121
closed
5 years ago
3
Update bucket location (resolves #168)
#169
jvivian
closed
5 years ago
0
Update location of test samples to new bucket
#168
jvivian
closed
5 years ago
0
Add better test samples (resolves #166)
#167
jvivian
opened
5 years ago
3
Swap out test sample for tests
#166
jvivian
opened
5 years ago
0
Fix broken Docker builds (resolves #164)
#165
jvivian
closed
5 years ago
0
Build broken on master
#164
jvivian
closed
5 years ago
0
Add BAM UMEND QC (resolves #157)
#163
jvivian
closed
5 years ago
2
Add BAM support to Docker wrapper
#162
jvivian
opened
5 years ago
2
Create test samples that cutadapt can run
#161
jvivian
closed
5 years ago
1
Move test files to courtyard server
#160
jvivian
closed
5 years ago
1
Update cutadapt to 1.18
#159
jvivian
closed
4 years ago
1
Add BAM umend QC
#158
jvivian
closed
5 years ago
0
Add BAM Umend QC as an option
#157
jvivian
closed
5 years ago
1
Update input links (resolves #155)
#156
jvivian
closed
5 years ago
0
Move workflow inputs back to S3
#155
jvivian
closed
5 years ago
2
Update gencode_hugo_map container to fix ZeroDivisionError when no genes map
#154
jvivian
closed
5 years ago
0
Change input creation to use `tarball_files`
#153
jvivian
closed
5 years ago
0
Add documentation for creating workflow inputs
#152
jvivian
closed
6 years ago
0
Add ability to handle mismatched fastq files
#151
jvivian
closed
5 years ago
1
Exception in thread Thread-641:
#150
hmkim
closed
6 years ago
3
docker: Cannot connect to the Docker daemon. Is the docker daemon running on this host?.
#149
hmkim
closed
6 years ago
1
Adjust disk requirements for several jobs (resolves #145)
#148
jvivian
closed
6 years ago
0
Create output directory if it doesn't exist (resolves #146)
#147
jvivian
closed
6 years ago
0
Check for output directory and create if necessary
#146
jvivian
closed
6 years ago
0
Adjust resource requirements
#145
jvivian
closed
6 years ago
0
Add Encapsulation for BAM Processing (Resolves #143)
#144
jvivian
closed
6 years ago
0
Fix race condition for Promise for BAM input
#143
jvivian
closed
6 years ago
0
Ownership error with squashed outputs
#142
fcomitani
opened
6 years ago
5
Pin gdc-client to quay.io image (resolves #140)
#141
jvivian
closed
6 years ago
0
Replace gdc-client Image
#140
jvivian
closed
6 years ago
1
Auto scaling in the pipeline without having to create a leader and rsync files
#139
wshands
closed
6 years ago
3
fix the misplaced doc string
#138
wshands
closed
6 years ago
0
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