prodigal process expects gzipped file
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bug
- Dominant language
- Nextflow
- Stars
- 119
- Forks
- 40
- Avg merge
- 2d 17h
- Merged PRs (30d)
- 5
Description
Description of the bug
The prodigal process expects a gzipped file, also the singularity environment doesn't contain pigz.
I can hack it by replacing the first instance of pigz with cat, and the subsequent pigz -nm ones with gzip -n, and replace the version echo at the end by a fixed random-ish string.
Command used and terminal output
Relevant files
No response
System information
No response
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
Locate the prodigal process and inspect how it handles gzipped input and invokes pigz inside the Singularity environment. Reproduce the failure with that process and determine the expected compression and version-reporting behavior; done means prodigal runs in the stated environment without the missing pigz dependency.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100