Input File Naming Convention
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- Dominant language
- Nextflow
- Stars
- 112
- Forks
- 68
- PR merge metrics
- No merged PRs in 30d
Description
there is a some sort of…bug (idk if i’d call it that) in naming the input files. Basically, if the file names contain a number by itself (for example, our data was named like xxx_HiC_2_S43_L007_R1.fastq.gz), there would be problem parsing the name during merging and subsequent steps.
I did not notice this with HiC-pro, only in nf-core/hic.
Contributor guide
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 by reproducing the nf-core/hic workflow with the example filename xxx_HiC_2_S43_L007_R1.fastq.gz, then inspect the input-name parsing and merging steps. Confirm where the standalone number is misinterpreted and test the subsequent workflow steps; done means these filenames parse and merge successfully without breaking later processing.
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
- Needs clarification
- Newbie friendliness
- 25/100