BD2KGenomics toil-rnaseq issues

BD2KGenomics / toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

Apache License 2.0

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issues

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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