Wrong capture of hash with filterNextflowOutput
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- Dominant language
- Java
- Stars
- 13
- Forks
- 11
- Avg merge
- 1d 16h
- Merged PRs (30d)
- 6
Description
This error message:
WARN: FASTQ file(/home/runner/tests/dbcf29769b30ade963f50358dd930f12/work/7b/b7421f705229baeb721b87806b97ed/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
Get saved as:
WARN: FASTQ file([PATH]/tests/[NFT_HASH]/work/22/[NFT_HASH]/test_R1_R2_R1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
Instead of:
WARN: FASTQ file([PATH]/tests/[NFT_HASH]/work/[NFT_HASH]/test_R1_R2_R1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
Which results in non reproducible results
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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 locating the filterNextflowOutput entry point and inspect how work-directory hashes are replaced in captured warning messages. Reproduce the example and verify that each work path component is normalized consistently, with no separate hash segment left unmasked.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- testing-qa, tooling
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100