Add WDL implementation for Salmon - #326

Merged

adthrasher merged 27 commits into

stjudecloud:mainfrom

PriyankaaXD:add-salmon-wdl

Sep 15, 2026

Commits on Aug 27, 2026

Update Salmon container image to a more current version
PriyankaaXD
committed
8a69a0e
Add Sprocket unit tests for Salmon WDL tasks
PriyankaaXD
committed
d89ca54
Fix fldMean/fldSD argument quoting and suppress SC2086 false-positive
PriyankaaXD
committed
58108ff
Move test file to tools/test/ and rename to .yaml extension
PriyankaaXD
committed
23aee50
Fix single-end quant mode (-r flag), rebuild test fixtures from shared FASTQ data, add SE test
PriyankaaXD
committed
61ca77b
Require non-empty array for read_one_fastqs_gz
PriyankaaXD
committed
211befd
Expose validateMappings as a Boolean input
PriyankaaXD
committed
7764bc0
Expose decoy-aware indexing as an optional input on build_salmon_index
PriyankaaXD
committed
b58e2f7
Make memory allocation dynamic for both tasks, based on input size
PriyankaaXD
committed
13b1847
Add CHANGELOG entry for Salmon WDL implementation
PriyankaaXD
committed
882635b
Document how Salmon test fixtures were generated
PriyankaaXD
committed
fd6f872
Rename gentrome variable to fasta, remove 'recommended' wording from decoys help text
PriyankaaXD
committed
4b73fad
Use existing repo reference FASTAs instead of synthetic transcripts, add decoy-aware indexing test
PriyankaaXD
committed
6d7bc7d
Update to Salmon v2.6.0, rebuild index fixture with new format
PriyankaaXD
committed
8aa822a
Revert fixture to v1 index pending maintainer decision on v2 fixture size
PriyankaaXD
committed
a5e46e8

Commits on Sep 4, 2026

Commits on Sep 9, 2026

Rename task to index, fix decoy conditional logic, add gzip symlink support, misc review fixes
PriyankaaXD
committed
1d2910e

Commits on Sep 11, 2026

chore: add ext help link
adthrasher
committed
c8f5157
nit: docs and test tags
a-frantz
committed
389eb05
fix sprocket TOML
a-frantz
committed
f798d2b
nit: idiomatic bash
a-frantz
committed
53e768d
chore: remove salmon-ignored flag
a-frantz
committed
5755914
chore: update to 1.3
adthrasher
committed
dc4f83d

Commits on Sep 14, 2026

chore: bump memory based on experimental results
adthrasher
committed
32ac3ed
chore: switch to hardcoded memory values for index
adthrasher
committed
ec51438