Add WDL implementation for Salmon by PriyankaaXD · Pull Request #326 · stjudecloud/workflows

PriyankaaXD · 2026-08-13T00:19:59Z

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

Tasks added in tools/salmon.wdl:

build_salmon_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 1.9.0. 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 · 2026-08-13T00:20:17Z

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adthrasher · 2026-08-13T13:20:54Z

+
+    runtime {
+        cpu: ncpu
+        memory: "16 GB"


Does salmon use a consistent amount of RAM or is it dependent on the input and/or transcriptome?

Sorry, I originally hardcoded 16 GB without thinking much about how the memory usage would actually vary.

Salmon's memory usage mainly depends on the index size, which depends on the transcriptome size and whether decoys are included. The input reads are streamed, so their size doesn't have as much impact on RAM usage.

I've now updated both build_salmon_index and quant to calculate memory_gb dynamically based on the input size, similar to how disk_size_gb is already handled. There's also a modify_memory_gb option if the estimate needs to be adjusted for specific data.

adthrasher · 2026-08-13T13:24:06Z

+            "~{if length(read_twos) == 0 then "--fldMean " + fld_mean else ""}" \
+            "~{if length(read_twos) == 0 then "--fldSD " + fld_sd else ""}" \


I don't think this will work as the arguments end up quoted in bash. Was this an attempt to address a sprocket lint warning?

adthrasher · 2026-08-13T13:32:06Z

This also needs a CHANGELOG entry.

…d FASTQ data, add SE test

a-frantz

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

a-frantz · 2026-08-23T20:07:55Z

@@ -0,0 +1,5 @@
+# Salmon test fixtures
+
+`transcripts.fasta` — synthetic transcripts built by concatenating real R1 + reverse-complemented R2 sequences from the shared `fastqs/test_R1.fq.gz`/`fastqs/test_R2.fq.gz` fixtures, ensuring genuine alignment for testing purposes.


the input to build_salmon_index can be just any FASTAs, so what you have here isn't invalid for any technical reason, however to closer replicate the real data (mostly for posterity rather than correctness) we can drop this transcripts.fasta file and instead use one of the existing .fa files from fixtures/reference/. Those aren't quite right either, as really the input to Salmon indexing should be from the transcriptome, and the fasta sequences we've already committed to the repo are from the genome.

Ideally, we should really be committing a new subsetted transcriptome reference and using one of the existing genome references as decoy sequences; but, this repo is already ginormous with all our reference test files and I'd rather not add a new FASTA when existing FASTAs will work fine.

Please uncommit this transcripts.fasta file, and regenerate salmon_index.tar.gz using one of the already committed .fa files (dealer's choice for which)

a-frantz · 2026-08-23T20:17:08Z

+        cpu: ncpu
+        memory: "~{ceil(transcripts_fasta_size * 4) + 4 + modify_memory_gb} GB"
+        disks: "~{disk_size_gb} GB"
+        container: "quay.io/biocontainers/salmon:1.9.0--h7e5ed60_0"


can we update to a Salmon-v2 container?

Quick note on the v2 migration: I updated the container and confirmed all our command-line flags remain compatible (both index and quant), and all 4 tests pass. But one thing worth flagging — the new SSHash-based index format is significantly larger than v1's for the same reference: our GRCh38.chrY_chrM.fa-based fixture went from 224MB (v1/pufferfish) to 1.15GB (v2/SSHash). Given the earlier concern about repo/LFS bloat, wanted to surface this before it lands — let me know if you'd still like to proceed with committing this larger fixture, or if you'd prefer a different approach (e.g., a smaller subset reference, or building the index fresh in CI rather than committing it).

wow, that size explosion is shocking! Pinging @adthrasher as he might find this interesting.

I did some digging this morning, and I think the reason a tiny ref FASTA is creating such a huge index is because we are using subsetted chromosomes from the genome as the reference sequences, where Salmon is expecting individual transcripts from the transcriptome. There is likely an exponential relationship between ref seq length and disk size.

Interestingly, when I tried passing the chr1_chr19 fasta as a decoy to the chrY_chrM build, the resulting index shrank by more than half.

Ultimately though, I think we should commit an appropriate transcriptome reference and use that here, instead of taking the lazy shortcut I suggested earlier 😅 I will create a usable ref FASTA from the human reference transcriptome and commit it to main, then you can rebase this PR and use the file I upload as an input to salmon index for the tests.

a-frantz · 2026-08-23T20:21:10Z

+        tar -czf "~{prefix}.tar.gz" "~{prefix}"
+    >>>
+
+    output {


can we also output the "raw" quant.sf file? - https://combine-lab.github.io/salmon/reference/output-formats/

this should be in addition the tarballed output. Some users will likely only care about the quant file, and for running a workflow the quant file may be the only one that's needed downstream so having to extract it from a tarball is a cumbersome intermediate step.

…decoys help text

…add decoy-aware indexing test

…size

_Describe the problem or feature in addition to a link to the issues._ This is needed for writing decent tests in #326 BCR and ABL1 were chosen somewhat arbitrarily. We do have other test fixtures referencing these genes specifically (tests are for Arriba), but this doesn't interact with those tests v50 release chosen as its latest. Other fixtures use v31; I could use that release if we want Before submitting this PR, please make sure: - [x] You have added a few sentences describing the PR here. - [x] 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! - [x] You have updated the README or other documentation to account for these changes (when appropriate).

PriyankaaXD mentioned this pull request Aug 13, 2026

tool wishlist #228

Open

adthrasher requested review from DelaramR, a-frantz and adthrasher August 13, 2026 13:14

adthrasher assigned PriyankaaXD Aug 13, 2026

adthrasher requested changes Aug 13, 2026

View reviewed changes

PriyankaaXD added 10 commits August 19, 2026 10:29

Update Salmon container image to a more current version

1332a54

Add Sprocket unit tests for Salmon WDL tasks

81f8293

Fix fldMean/fldSD argument quoting and suppress SC2086 false-positive

5282101

Move test file to tools/test/ and rename to .yaml extension

c07cb93

Fix single-end quant mode (-r flag), rebuild test fixtures from share…

3d2e4a5

…d FASTQ data, add SE test

Require non-empty array for read_one_fastqs_gz

d3c3c24

Expose validateMappings as a Boolean input

581ac93

Expose decoy-aware indexing as an optional input on build_salmon_index

fa9d808

Make memory allocation dynamic for both tasks, based on input size

449001d

Add CHANGELOG entry for Salmon WDL implementation

4f222d5

PriyankaaXD force-pushed the add-salmon-wdl branch from c2d9dde to 4f222d5 Compare August 19, 2026 05:17

Document how Salmon test fixtures were generated

cc2177c

PriyankaaXD requested a review from adthrasher August 19, 2026 05:53

a-frantz requested changes Aug 23, 2026

View reviewed changes

PriyankaaXD added 4 commits August 24, 2026 10:19

Rename gentrome variable to fasta, remove 'recommended' wording from …

6020a4e

…decoys help text

Use existing repo reference FASTAs instead of synthetic transcripts, …

e1713ee

…add decoy-aware indexing test

Update to Salmon v2.6.0, rebuild index fixture with new format

964b3e9

Revert fixture to v1 index pending maintainer decision on v2 fixture …

71e9c9a

…size

a-frantz mentioned this pull request Aug 25, 2026

test: transcript sequences fixture #330

Merged

6 tasks

		"~{if length(read_twos) == 0 then "--fldMean " + fld_mean else ""}" \
		"~{if length(read_twos) == 0 then "--fldSD " + fld_sd else ""}" \

		@@ -0,0 +1,5 @@
		# Salmon test fixtures

		`transcripts.fasta` — synthetic transcripts built by concatenating real R1 + reverse-complemented R2 sequences from the shared `fastqs/test_R1.fq.gz`/`fastqs/test_R2.fq.gz` fixtures, ensuring genuine alignment for testing purposes.

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PriyankaaXD commented Aug 13, 2026

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adthrasher commented Aug 13, 2026

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stjudecloud-cloudy commented Aug 13, 2026 •

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