A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I've been told that "`java.nio.file` seems to need a file-system path rather than a URL, so if one of the inputs is meant to be a filepath rather than a URL, you may need to download and save as a file manually and supply that path as an input.  Or there's a problem in the pipeline that isn't correctly converting the URI to a path." does this make sense to you?

This is probably coming from <https://github.com/nf-core/riboseq/blob/3d3e57978c5e0a418e56728496b6cc12700e6443/subworkflows/local/prepare_genome/main.nf#L208|here>, and we've been using this with all our testing, so I'm disinclined to believe that URIs are the problem there.

Can I ask what infrastructure you're running this on? Is it possible that Nextflow is running in an environment without access to the internet?

I'm using Linux-based high-performance storage and computing system scheduled using SLURM. Is this what you are after? I'm checking with our system support internet access from the compute nodes.

the error still reads as thought the java library expects that file to be local and doesnt recognise that it is a url. which could be a version of java - the java version is loaded in the nextflow module. Is there a minimum version of java that it's required to run the pipeline?

I doubt that's the issue here, Nextflow's `file()` method works just fine with URIs and this workflow has test infrastructure that demonstrates clearly that this works. It _may_ be something with your local Java (sorry, out of my depth there so I won't personally be any help), but it's definitely worth checking that the file is accessible from wherever the Nextflow process is running. If it's not, there mechanisms to work around that.

agree, this could be a `Java` version issue.  what `Java` version (and `Nextflow` for that matter) are u using?

FYI, i can reproduce the error with `-r 1.0.0` and `test` profile using `Nextflow 23.10.0` and
```openjdk 11.0.2 2019-01-15
OpenJDK Runtime Environment 18.9 (build 11.0.2+9)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.2+9, mixed mode)```
yielding
```ERROR ~ No such file or directory: <https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta>```
The error disappears if explicitly loading `Java 17` after loading `Nextflow`.

Hi Ira, thank you for checking this out. I'm using: Currently Loaded Modules:
 1) Java/11.0.2  2) Nextflow/23.10.0  3) Singularity/3.6.4

yes, Java 11 isnt working it seems, try to use a later version of Java if available on your system

Thanks for chasing that down Ira :slightly_smiling_face: