Add WDL implementation for Salmon

[PriyankaaXD]

Adds a WDL implementation for Salmon (mapping-mode only), per the "tool wishlist" issue #228.

Tasks added in tools/salmon.wdl:

• index — wraps salmon index
• quant — wraps salmon quant

All "important options" from Salmon's docs are exposed as inputs, with defaults verified against salmon quant --help-reads output on Salmon 2.6.0. Parameter documentation is copied from Salmon's official docs, per guidance in the issue. Scoped to mapping-mode only (FASTQ input) — no BAM/alignment-mode support, as requested.

Tests added in tools/salmon.yml using the new Sprocket test framework, covering both tasks with real output assertions. Verified locally: sprocket lint passes cleanly, sprocket dev test passes both tests.

This is my first contribution to this project — happy to make any adjustments you'd like!

Before submitting this PR, please make sure:

• You have added a few sentences describing the PR here.
• The code passes all CI tests without any errors or warnings.
• You have added tests (when appropriate).
• You have added an entry in any relevant CHANGELOGs (when appropriate).
• If you have made any changes to the scripts/ or docker/ directories, please ensure any image versions have been incremented accordingly!
• You have updated the README or other documentation to account for these changes.

[stjudecloud-cloudy]

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[adthrasher]

This also needs a CHANGELOG entry.

[a-frantz]

This is looking really great! Left some comments to address, but this is close to the finish line 🚀

[a-frantz]

looking really good 🚂

[PriyankaaXD]

since I iterated on the index fixture several times (custom → v1 → v2 → reverted → BCR/ABL1), my branch's LFS history now carries a few superseded large blobs (~1.3GB total across old versions) even though the current file is tiny. If you squash-merge, this shouldn't carry into main's history — let me know if you'd prefer I try to clean this up

[a-frantz]

If you squash-merge, this shouldn't carry into main's history — let me know if you'd prefer I try to clean this up

we'll do a squash-merge 👍 no action needed on your end

[a-frantz]

Good news: we're at the nitpicking stage of the review 🤣 Left a bunch of comments, but all of them are about very minor things. This looks great 🚀

[PriyankaaXD]

Just a quick note - builds_index_with_decoys fails locally for me on Windows with Unsupported reparse point type when reading back a symlink created inside the container. Manually confirmed the symlink itself is created correctly on the Linux side (via docker run ... ln -sf ...), so this looks like a Windows-host/Docker-volume limitation on my end, not an actual bug — should be fine in your CI, but flagging in case you want to verify.

[a-frantz]

@PriyankaaXD I just pushed some small nits I wanted in before merge but didn't want to force us through another round of back and forth for such minor points. Hope you don't mind!

@adthrasher could you give this an additional review?

[PriyankaaXD]

Thanks for testing at production scale — good catch that decoys need to factor into the memory calc more heavily. Happy to update the formula to include decoys_fasta_size once you've got final numbers, or if you'd rather just push the tuned value yourself given you already have the real data, that works too!

[adthrasher]

Finished quant runs for reference with and without decoys.

    #0   completed wall  338m00s  queued    30.6s  4 cpu, 31.7 GiB  peak 10.9 GiB, cpu 1337m03s
    #0   completed wall  360m59s  queued    31.5s  4 cpu, 10.2 GiB  peak 4.3 GiB, cpu 1432m16s

[adthrasher]

Thanks @PriyankaaXD for implementing this!