nasa / nasa/GeneLab_Data_Processing
[Amplicon Illumina] Issue with datasets that have multiple assays of the same target
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 125
- Forks
- 65
- PR merge metrics
- No merged PRs in 30d
Description
When running the pipeline from the DEV_Amplicon_Illumina_NF_conversion branch using datasets with multiple assays for the same target (ex. OSD-417), it is failing to create a runsheet (at GET_RUNSHEET process) with the following error:
In addition, the --specify-runsheet argument cannot be passed to the pipeline as it is not part of the pipeline's declared parameters.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in the DEV_Amplicon_Illumina_NF_conversion branch under Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-C and inspect the GET_RUNSHEET process. Reproduce the failure with dataset OSD-417 and check how the --specify-runsheet argument is declared. Done means the pipeline creates a runsheet for multiple assays of the same target and accepts the argument.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100