[FEATURE] STAR handle gzipped files
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Description
Is your feature request related to a problem? Please describe
I'd be cool if we didn't have to include
withName: STAR_ALIGN {
ext.args = '--readFilesCommand zcat'
}
Describe the solution you'd like
def gzip = reads.name.endsWith(".gz") ? "--readFilesCommand zcat"
"""
STAR \\
--genomeDir $index \\
--readFilesIn $reads \\
--runThreadN $task.cpus \\
--outFileNamePrefix $prefix. \\
$out_sam_type \\
$ignore_gtf \\
$seq_center \\
$gzip \\
$args
I can't remember if : is necessary or not in the Elvis operator.
Describe alternatives you've considered
- Not doing this and leaving it up to users to figure it out.
- We might want to handle overriding that with
args2maybe or some other method that checks theext.argsfor a--readFilesCommand
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 STAR_ALIGN module and reading how its command is assembled, including the existing ext.args and args2 handling. Confirm the intended behavior for .gz reads and how an explicit --readFilesCommand override should work; done means gzipped inputs are handled automatically without breaking user overrides.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100