INTERPROSCAN fails with real database: version mismatch and nested data directory #114

Description of the bug

With the default InterProScan database settings, INTERPROSCAN fails on a real (non-test) run:

Running hmmpress (/usr/local/bin//hmmpress) on data/pirsf/3.10/sf_hmm_all
failed to open SSI index data/pirsf/3.10/sf_hmm_all.h3i
Could not run hmmpress!
...
FATAL - Analysis step 27 : Run pirsf.pl binary for selected proteins for proteins 1 to 405 has failed irretrievably.

CI doesn't catch it because the test profiles use the small interproscan_test.tar.gz.

Causes

1. Container and database versions don't match (confirmed)

• modules/nf-core/interproscan/main.nf uses the interproscan:5.59_91.0 container.
• nextflow.config sets interproscan_db_url to the 5.72-103.0 release.

InterProScan reads member database paths from its bundled interproscan.properties. The 5.59 container therefore looks for data/pirsf/3.10, data/panther/17.0, data/tigrfam/15.0 and so on, none of which exist in the 5.72 data. TIGRFAM was also merged into NCBIfam after 5.59, so the default interproscan_applications depends on the version.

2. The staged database directory is probably nested one level too deep (likely, not yet confirmed)

The full EBI release tarball contains a single top-level folder interproscan-X/ holding bin/, data/, interproscan.sh and so on. UNTAR strips that folder, and the module then stages the whole install directory as data (stageAs: 'data'). The HMMs end up at data/data/pirsf/..., while InterProScan looks for data/pirsf/.... The test tarball has no wrapper folder, which would explain why tests pass.

The same failure happens after switching the URL to the matching 5.59 release.

3. The HMMs aren't pre-pressed

Release tarballs need python3 setup.py -f interproscan.properties to be run once. Without it, pirsf.pl runs hmmpress inside the shared UNTAR output while the pipeline runs. With several input FASTAs, parallel INTERPROSCAN tasks can press the same files at the same time and race.

Suggested fix

• Keep the container and interproscan_db_url on the same version. Either bump both to 5.72 once the container is available (see Bump interproscan in bioconda #20) and replace TIGRFAM with NCBIfam, or point the URL at the 5.59-91.0 release.
• In subworkflows/local/functional_annotation/main.nf, pass the inner data/ folder when it exists, for both the download branch and the --interproscan_db branch:

  .map { _meta, database -> database.resolve('data').exists() ? database.resolve('data') : database }

• Press the HMMs once after UNTAR, with a small local step running setup.py, or document that --interproscan_db must point to a database that has already been set up.

Command used and terminal output

Slurm HPC, Singularity, default interproscan_db_url and interproscan_applications (Hamap,PANTHER,PIRSF,TIGRFAM,sfld), --disable-precalc.

System information

• Pipeline: dev (ffb0473)
• Executor: Slurm
• Container engine: Singularity
• InterProScan container: 5.59-91.0