Conversation
Joon-Klaps
left a comment
Joon-Klaps
left a comment
There was a problem hiding this comment.
Nice addition! Minor suggestions.
Wondering if this is actually not a subcommand of a larger tool bio2zarr, which would make the name of the tool modules/nf-core/bio2zarr/vcfpartition, thoughts?
| sanitizeOutput(process.out), | ||
| file(process.out.partitions[0][1]).readLines().size(), | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
There was a problem hiding this comment.
| sanitizeOutput(process.out), | |
| file(process.out.partitions[0][1]).readLines().size(), | |
| process.out.findAll { key, val -> key.startsWith("versions") } | |
| sanitizeOutput(process.out), |
You're snapshotting the entire ouput, so we can remove individual file checks
There was a problem hiding this comment.
You're right - I wanted to be able to see the number of partitions at a glance - since:
Note that both the number of partitions and sizes are a target, and the returned number of partitions may not exactly correspond 1.
Happy to remove!
Footnotes
| file(process.out.partitions[0][1]).readLines().size(), | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
There was a problem hiding this comment.
| file(process.out.partitions[0][1]).readLines().size(), | |
| process.out.findAll { key, val -> key.startsWith("versions") } |
| file(process.out.partitions[0][1]).readLines().size(), | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
There was a problem hiding this comment.
| file(process.out.partitions[0][1]).readLines().size(), | |
| process.out.findAll { key, val -> key.startsWith("versions") } |
| file(process.out.partitions[0][1]).readLines().size(), | ||
| process.out.findAll { key, val -> key.startsWith("versions") } |
There was a problem hiding this comment.
| file(process.out.partitions[0][1]).readLines().size(), | |
| process.out.findAll { key, val -> key.startsWith("versions") } |
modules/nf-core/vcfpartition/main.nf
Outdated
| tuple val(meta), path("*.icf"), emit: icf | ||
| tuple val("${task.process}"), val('vcf2zarr'), eval('vcf2zarr --version |& sed -n "s/.* //p"'), emit: versions_vcf2zarr, topic: versions | ||
| tuple val(meta), path("*.tsv"), emit: partitions | ||
| tuple val("${task.process}"), val('vcfpartition'), eval("vcfpartition --version | sed 's/vcfpartition, version //'"), topic: versions, emit: versions_vcfpartition |
There was a problem hiding this comment.
| tuple val("${task.process}"), val('vcfpartition'), eval("vcfpartition --version | sed 's/vcfpartition, version //'"), topic: versions, emit: versions_vcfpartition | |
| tuple val("${task.process}"), val('vcfpartition'), eval("vcfpartition --version | sed 's/.* //'"), topic: versions, emit: versions_vcfpartition |
Good question. I think one argument is that I previously added the modules vcf2zarr/convert and vcf2zarr/explode. I didn't consider the other tools then, but now I want to work on |
|
Or, more simply, there is no |
Are there other commands within the But even then, if
I see why you would opt for that here though... it's a bit nasty from the developers... When did you add the previous modules? Do you think they are already being used in pipelines, or are they fresh modules that we could rename them (e.g. to `bio2zarr/vcf2zarrexplode)? Another annoying example i've encoutnered is the conda recipe being called But let's also see what other maintainers think... ultimately it's about findabilty at this poitn |
|
One yesterday, one last year. Neither used in pipelines as far as I can tell.
|
3 participants
PR checklist
Closes #11097 by adding new module: vcfpartition
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda