[FEATURE] FASTQSCREEN_FASTQSCREEN should accept multiple inputs with a single database
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Description
Is your feature request related to a problem? Please describe
When you provide an input channel of fastq files to FASTQSCREEN_FASTQSCREEN, only the first one is run because there is only one database.
Describe the solution you'd like
I think you need to accept database as a value and allow it to not limit the execution, e.g. with each statement. In the tests it is always tested with a single input, so probably would be a good idea to update those too.
Describe alternatives you've considered
One could repeat the input database path as many times as many reads there are, but that is a workaround and a hacky solution.
Or the input can be tuple val(meta), path(read), path(database) so that with combine() it can be solved.
Additional context
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
Start by locating the FASTQSCREEN_FASTQSCREEN module and its existing tests, then inspect how the input channel and database value are consumed. Update the behavior so multiple FASTQ inputs can run with one database, and extend the tests beyond the current single-input case.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100