nf-core
Launching one-off subworkflows
Anyone have any ideas how we can pass the input channels in?
Workflow `ALIGN_BOWTIE2` declares 2 input channels but 0 were specified
Anyone have any ideas how we can pass the input channels in?
Workflow `ALIGN_BOWTIE2` declares 2 input channels but 0 were specified
I've tried several variations and so far nothing works. I came to the conclusion it wasn't possible to pass anything to take, except by using another script.
Can this work though?
Consider if this snippet was at the bottom of main.nf:
workflow {
ALIGN_BOWTIE2(
params.reads // channel: [ val(meta), [ reads ] ]
params.index // channel: /path/to/bowtie2/index/
)
}
How would one tell Nextflow the string path is actually a file path?
I have a feeling we need something like https://www.nextflow.io/docs/edge/dsl2.html#module-templates And then we can call a template that handles the file input params, or maybe something that just takes a samplesheet and outputs a meta map like channel, and then we pass in the subworkflow name in the template.
Doesn't that mean the process has to take care of the file staging Nextflow usually does? Otherwise what's the difference to writing another anonymous workflow which calls the named workflow?
That was all that I was imagining the template would be is an anonymous workflow, that might hook it up to a samplesheet module or something. Your snippet might work with fromfilepairs and maybe some magic to turn the name into a meta.id
Shall we close this one, as I'm assuming it's no longer relevant. @Emiller88 @mahesh-panchal
I think it's even more relevant now that we've actually added subworkflows
Hi there!
We've noticed there hasn't been much activity here. Are you still planning on working on this? If not, you can ignore this message and we'll close your PR in about 2 weeks
Cheers the nf-core maintainers
