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

nf-core

Hi,
I'm updating the `ichorcna` module to topic versions.
However this module calls in R seqInfo(genome_build) and this function try to download a file on UCSC.
This download then fail on the github's CI.
What should I do ?
<https://github.com/nf-core/modules/pull/11829>

What I don't understand is that at first it did work for singularity and docker in the CI
<https://github.com/nf-core/modules/actions/runs/26772064983/job/78914080261>

Should I rewrite the whole function in a template to remove the seqInfo call and pass it with a chrom_size table (downloaded beforehand) ?

I would move on and focus on other modules personally

I definitely encountered this issue myself ~3 years ago

But, this would left a module without the topic ! :smiling_face_with_tear:
Or should we simply force push with a message saying this module doesn't work without internet access ?

Luca may have encountered this more recently too <@U04RCVAGTU7>

If the CI has internet access, this is really strange.
A simple
```download.file(
    "<https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz>",
    tempfile()
)```
gives an error, while locally it works

I can download it on my macbook, but not from my server

So it seems that <https://hgdownload2.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz>, <https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz> are reachable from the CI but not, <https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz>

But even thought the `Seqinfo(genome)` function calls `getOption("UCSC.goldenPath.url")` , setting `options(UCSC.goldenPath.url = "<https://hgdownload2.soe.ucsc.edu/goldenPath>")` still leads to `cannot open URL '<https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz>'` ...
What the hell :melting_face:

probably being overwritten: <https://github.com/Bioconductor/GenomeInfoDb/blob/devel/R/zzz.R>

Yeah, to fix it we need to load the library first, then update the options.

Strange, this did work in the CI by doing
```library("GenomeInfoDb")
options(UCSC.goldenPath.url = "<https://hgdownload2.soe.ucsc.edu/goldenPath>")
Seqinfo(genome="hg19")```
<https://github.com/nf-core/modules/pull/11829>

Weird that I didn't notice it, SAMURAI uses it verbatim I think

the server was accessible from some locations, just not all