update module: HISAT2/ALIGN

[RaqManzano]

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?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Are you going to work on this?

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

[OlivierCoen]

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

[RaqManzano]

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

Yep

[OlivierCoen]

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

[sguizard]

Hi all,
I fell on the same problem.

I think it's possible, as temporary solution, to inject the option through a module config via ext.args.
I'm going to test that and give a feedback.

For a more permanent solution, it might be possible to default the --temp-directory to . or set it with the TMPDIR variable.
I'm going to have a look to the module code and PR a decent solution when it's ready.

Cheers

[sguizard]

OK, I understand why the container.

The --temp-directory option has been implemented and merged into the master branch by the author, but no release has been made yet. In consequence the NFC module can't accepts this option.

I'm going to request a release to the author, which should trigger the bioconda package build, which triggers the singularity image build and should trigger the wave hisat2+samtools container.

[OlivierCoen]

Oh it's not been released yet, ok I see the problem now. Sorry for the off-topic comment

[sguizard]

@OlivierCoen No worries :) It's in process.

The author has made the new release of hisat2.
This has triggered the build of the bioconda package, which is available now.
Now it's possible to build wave container on the Sequera container space.

I'm presently testing a new container with the last version of hisat2 with a colleague that run a full scale analysis.

As soon as I have a successful test, I'll update the nf-core module.

FYI: we are testing this for moment

process {
        withName: HISAT_ALIGN {
                container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c3/c36472269e8898f63b7b65dd40433462d541f9e75f9401f0bf8488021275d006/data'
                ext.args = "--temp-dir ./tmp"
        }
}