update module: HISAT2/ALIGN

Open RaqManzano opened this issue 1 month ago • 3 comments

Why the update

There is an issue with how hisat2 handles tmp memory. In an HPC environment, when many jobs are running in the same cpu it is easy to run into this error (ERR): mkfifo(/tmp/46.inpipe1) failed. This bug is described in this HISAT2 issue. HISAT2 now has added --temp-directory that fixes this. However, this means that the container needs to be updated in order to be used. I have created a new container already that I have tested and works. Using this updated container makes the option --temp-directory available, which should be added to hisat2_align config as --temp-directory . to have the current working directory as temp.

Is there an existing module for this?

[x] I have searched for the existing module

Is there an open PR for this?

[x] I have searched for existing PRs

Is there an open issue for this?

[x] I have searched for existing issues

Are you going to work on this?

[x] If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

Dec 01 '25 16:12 RaqManzano

HI! What is specific to the container you made? Did you just install the latest versions of HISAT2 / samtools?

Dec 09 '25 06:12 OlivierCoen

HI! What is specific to the container you made? Did you just install the latest versions of HISAT2 / samtools?

Yep

Dec 09 '25 10:12 RaqManzano

Then you don't need to create a container yourself, you can directly use the Seqera containers: https://seqera.io/containers/ If you want, you can update the module yourself: https://nf-co.re/docs/tutorials/nf-core_components/components

Dec 09 '25 13:12 OlivierCoen