Option --unmapped does not run Bismark with --unmapped argument
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bug
- Dominant language
- Nextflow
- Stars
- 198
- Forks
- 181
- Avg merge
- 6d 17h
- Merged PRs (30d)
- 1
Description
Description of the bug
The current code does not correctly use the argument "--un" to run Bismark to save unmapped reads when the pipeline parameter "--unmapped" is specified. Unmapped reads are therefore not saved when requested. Checking the .command.sh script in the relevant work folder, the argument is not included in the Bismark align command.
Command used and terminal output
Relevant files
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System information
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Contributor guide
First steps
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Research direction
Locate the Bismark alignment entry point and the pipeline's --unmapped parameter, then inspect the generated .command.sh mentioned in the report. Verify that requesting --unmapped results in the Bismark command receiving --un and that unmapped reads are saved.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100