feat(simpleaf): bump to 0.25.0 with Seqera Wave container and topic-channel versions

[an-altosian]

Summary

• Updates simpleaf/index and simpleaf/quant modules to simpleaf 0.24.1 using a Seqera Wave / Community container.
• Migrates the versions output from the legacy versions.yml file to the new topic-channel convention (matches t1k/build).
• Realigns environment.yml pins with what the container actually ships, including removing the no-longer-required salmon dependency.

Container

Type	URI
Docker	community.wave.seqera.io/library/simpleaf:0.24.1--41e05fd46d838d92
Singularity / Apptainer	https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/83/83ab36a4aba7f26860f96dd73bb428a4a4eb05450c4cfc9488cf77adefad1adb/data

Key changes

Versions / dependencies

• simpleaf 0.19.5 → 0.24.1
• alevin-fry 0.11.2 → 0.14.0 (matches container)
• piscem 0.12.2 → 0.20.0 (matches container)
• salmon removed — simpleaf 0.24.x's piscem-only pipeline does not depend on salmon, and the Wave container does not ship it. The previous emit silently produced an empty version string because $(salmon --version) errored silently inside the cat <<-END_VERSIONS heredoc.

Topic-channel versions

Both main.nf files now emit each tool's version as a separate topic-channel tuple instead of writing versions.yml:

```groovy
tuple val("${task.process}"), val('alevin-fry'), eval("alevin-fry --version | sed 's/alevin-fry //'"), topic: versions, emit: versions_alevin_fry
tuple val("${task.process}"), val('piscem'), eval("piscem --version | sed 's/piscem //'"), topic: versions, emit: versions_piscem
tuple val("${task.process}"), val('simpleaf'), eval("ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'"), topic: versions, emit: versions_simpleaf
```

The ALEVIN_FRY_HOME=. prefix is needed because the eval() directive runs in a separate shell context from the script block where the env var is exported.

Test updates

• piscem 0.20 produces a new on-disk index format. The legacy .sshash / .json files were replaced by .ssi / .ssi.mphf / _ver.json / .sigs.json / .tct / .tdct. Assertions in main.nf.test and the corresponding stub touch lines have been updated.
• Snapshot assertions migrated from snapshot(process.out.versions).match() to snapshot(process.out.findAll { key, val -> key.startsWith(\"versions\") }).match() to capture the new per-tool topic emits.
• meta.yml regenerated via nf-core modules lint --fix; obsolete versions: - versions.yml stanza removed by hand.

Test plan

• nf-test test modules/nf-core/simpleaf/index/tests/main.nf.test --profile docker — 5/5 PASS
• nf-test test modules/nf-core/simpleaf/quant/tests/main.nf.test --profile docker — 2/2 PASS
• nf-core modules lint simpleaf/index — 0 failures
• nf-core modules lint simpleaf/quant — 0 failures

Note on residual lint warnings

A separate PR comment below explains the residual main_nf_container and container_links warnings, which are upstream nf-core/tools quirks that surface on every Seqera Wave module (e.g. t1k/build, ngsbits/*) and are not actionable at the module level.

[an-altosian]

Note for reviewers: residual nf-core modules lint warnings

This PR adopts a Seqera Wave / Community container per the nf-core Seqera Containers docs. Two lint warnings remain after this PR and are not actionable at the module level — they're known artifacts of nf-core/tools predating the Wave URL formats. Including them here so reviewers don't have to re-investigate.

1. main_nf_container: Container versions do not match

Cause: The lint check at nf_core/modules/lint/main_nf.py:360-384 parses the Singularity tag with the regex (?:[:.])?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$. For our Wave Singularity URL https://community-cr-prod.seqera.io/.../sha256/<hash>/data, that regex captures the literal string \"data\". The Docker tag regex captures \"0.24.1--41e05fd46d838d92\". Comparison \"data\" == \"0.24.1--41e05fd46d838d92\" → False → warning.

The check was designed for biocontainers-style URLs (…/fastqc:0.11.9--0) where both URLs end with the same version--build suffix. Wave's content-addressable blob URLs have no version substring at all.

2. container_links (HTTP 404)

Cause: Lint does a naked HTTP HEAD against the Docker URL. Wave's community registry doesn't answer with 200 on that endpoint — it requires an OCI manifest GET with Accept: application/vnd.oci.image.manifest.v1+json plus a token negotiation. docker pull / singularity pull / nextflow run all handle that handshake correctly. nf-test in this PR successfully pulled and ran the container end-to-end.

Reproducibility

Both warnings reproduce on every existing Wave-container module in the repo:

• modules/nf-core/t1k/build (the gold-standard topic-channel example)
• modules/nf-core/ngsbits/bedannotategc, and other ngsbits modules
• … and approximately 70 other modules already on Wave

Related upstream issues

• nf-core/tools#3179 — Download: Fix support for Seqera Community Containers (CLOSED, but documents that Wave Docker and Singularity URLs legitimately have different SHA values)
• nf-core/tools#3656 — Enable configurations for module linting (OPEN — proposes granular per-check disabling, which would let modules opt out of these specific Wave-related warnings)
• nf-core/tools#1377 — Modules linting 'Container versions do not match' (CLOSED 2021, addressed an older biocontainers-format mismatch; the fix didn't anticipate Wave URLs)

What this PR does NOT include

I did not file a new upstream issue specifically for the Wave version-mismatch case — happy to do so if reviewers want one to track. The structural cause is documented in #3179 and the workaround would naturally land in #3656.