Comments (1)
In particular, this was frequently causing InferStrandedness to fail, since CountObjects was often being submitted just before, but there are other points in the pipeline where this can happen.
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Related Issues (20)
- Add support for running SPEAQeasy with one sample
- allow starting the workflow with existing read alignments (sorted BAM/CRAM files) HOT 3
- InferStrandness failure, --force_strand not supported HOT 3
- Construct `rse_tx` for rat HOT 5
- `BuildAnnotationObjects` halts with current version of R
- Add support for more executors
- Improve or clarify what's supported for custom annotation
- PullTranscriptFasta failing HOT 1
- BuildAnnotationObjects fails HOT 19
- [JHPCE] repeated fastqc failure on trimmed paired data HOT 15
- Guide for all setups that are atypical in some way
- Develop a 1 day (max 2) workshop
- Videos documenting how to install and run SPEAQeasy + describing outputs
- Translate course and intro documentation to Spanish
- Add support for MultiQC and maybe other tools
- Add QC metrics generated by Monorail / recount3
- Adapt code to DSL2
- Create a contribution guidelines documentation
- improve storage usage, minimize duplication of FASTQ data HOT 2
- transcript quantification (Salmon/Kallisto) should use trimmed reads HOT 1
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