salmon

TAFFISH app for Salmon, a fast transcript-level RNA-seq quantification tool from COMBINE-lab.

Package Identity

Field	Value
name	salmon
command	taf-salmon
kind	tool
TAFFISH version	2.6.0-r1
container image	ghcr.io/taffish/salmon:2.6.0-r1
TAFFISH app license	Apache-2.0
upstream	COMBINE-lab/salmon
upstream release	v2.6.0
upstream commit	3e5ccb29caa7c25d72f3b17cc3cd21ddbb6dac7f
upstream license	BSD-3-Clause
runtime version	salmon 2.6.0
native platforms	linux/amd64, linux/arm64

Installation

Refresh the local Hub index and install the app:

taf update
taf install salmon

TAFFISH uses the configured container backend. To select one for a run:

TAFFISH_CONTAINER_BACKEND=podman taf-salmon -- --version
TAFFISH_CONTAINER_BACKEND=docker taf-salmon -- --version

Both declared Linux platforms use native upstream binaries; neither backend needs architecture emulation for linux/amd64 or linux/arm64.

What Is Included

This app packages the official Salmon v2.6.0 Rust CLI Linux release binaries:

• salmon-cli-x86_64-unknown-linux-gnu.tar.xz
  • SHA256: 898b9114c9901213d486ed5aac8cf9e9b8b6d5a52f0ed3e61ec441a044090ca5
• salmon-cli-aarch64-unknown-linux-gnu.tar.xz
  • SHA256: a642ddaeb4ba00f77ab5910589cbc675f7021f2bf9208858ae1b6d3d547391d3

The Dockerfile selects the correct upstream asset from Docker TARGETARCH, verifies the checksum, installs the upstream salmon binary under /opt/salmon/salmon, records immutable source identity in /opt/salmon/share/source.txt, and exposes it as /usr/local/bin/salmon. During a cross-architecture Buildx build, checksum and provenance checks still run, but target-binary execution is deferred to runtime smoke. Native builds run only the stable version, ordinary-help, provenance, and ldd build-time checks; real index and quantification paths remain runtime-only.

Salmon 2 is a from-scratch Rust rewrite. It keeps the core salmon index -> salmon quant -> quant.sf workflow and downstream quantification table formats, but it is a new major version with intentional breaking changes.

The runtime image uses the pinned multi-architecture debian:13-slim manifest sha256:d7e12182ce18b85b93007c1dedf31f2d29e01ccf3182cc4017c709b6259bc132 and the official Linux GNU binary. The v2 binary is much lighter than the old C++ distribution and depends only on the standard GNU runtime libraries available in Debian 13, notably libgcc_s, libm, and libc. The runtime also includes procps, matching upstream's workflow container compatibility support for tools such as Nextflow that probe ps.

Basic Usage

Show TAFFISH wrapper help:

taf-salmon --help

Show upstream Salmon help and version:

taf-salmon -- --help
taf-salmon -- --version
taf-salmon salmon --help
taf-salmon salmon --version

Current TAFFISH automatic command mode reconstructs a shell command line. If a path contains whitespace, ordinary outer-shell quoting alone is insufficient; include literal single quotes inside that argument:

taf-salmon salmon quant \
  -i "'indexes/salmon index'" -l A \
  -r "'reads/sample 1.fq.gz'" \
  -o "'results/sample 1'" -p 8

The inner single quotes are intentional. Prefer whitespace-free paths when possible.

Build a Salmon 2 index:

taf-salmon salmon index \
  -t transcripts.fa \
  -i salmon_index \
  -k 31 \
  -p 8

Quantify single-end reads:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  -o sample_quant \
  -p 8

Quantify paired-end reads:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -1 reads_1.fq.gz \
  -2 reads_2.fq.gz \
  -o sample_quant \
  -p 8

For compressed reads, -p is the shared execution-slot budget for decoding and mapping. Salmon chooses a serial or parallel decoder automatically. To override that decision or supply a reviewed policy file:

taf-salmon salmon quant \
  -i salmon_index -l A -r reads.fq.gz \
  --decoder serial \
  --threadPolicy thread-policy.json \
  -o sample_quant -p 8

--decoder accepts auto, serial, parallel, or parallel=N. Compression is detected from file content rather than the extension for reads, targets, alignments, and gene maps; supported formats include gzip/BGZF, bzip2, xz, and zstd. A plain or non-seekable input falls back to serial decoding.

Use the Salmon 2 sketch mode:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  --sketch \
  -o sample_sketch_quant \
  -p 8

Write RAD mappings while quantifying:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  --writeRad sample.rad \
  -o sample_quant \
  -p 8

Quantify a RAD file directly:

taf-salmon salmon quant \
  --rad sample.rad \
  --fldPolicy prior \
  --fldMean 250 \
  --fldSD 25 \
  -o sample_rad_quant \
  -p 8

Export retained mappings as unsorted BGZF BAM or SAM while quantifying:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  --writeBam mappings.bam \
  --bamCompressThreads 2 \
  -o sample_quant \
  -p 8

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  --writeSam mappings.sam \
  -o sample_quant_sam \
  -p 8

--writeBam and --writeSam preserve Salmon's retained mappings. They do not sort or index the output; use a downstream alignment tool when that is needed.

Salmon 2.6 performs deterministic FASTQ quantification by default:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  -o sample_deterministic_quant \
  -p 8

The retained --deterministic flag is accepted as a no-op for existing scripts. quant.sf is byte-identical across runs and thread counts. The deprecated --online option selects the pre-2.6 one-pass path and is scheduled for removal in Salmon 2.7.

The default path writes an lz4-compressed intermediate RAD and deletes it on success. Use --radScratchDir /path/to/scratch to place that temporary file on another volume, or --radCompress zstd for stronger compression. --skipQuant stops after mapping and keeps the RAD under the output directory as the run's deliverable; it does not write quant.sf.

Enable the opt-in SQUAREM or DAAREM EM/VBEM accelerator for slow-mixing problems or bootstrap-heavy workloads:

taf-salmon salmon quant \
  -i salmon_index \
  -l A \
  -r reads.fq.gz \
  --emAccel squarem \
  -o sample_accelerated_quant \
  -p 8

Use --emAccel daarem for the damped Anderson implementation. The default is none; both accelerators are opt-in and converge to the same fixed point, but their output is not byte-identical to the default at convergence tolerance.

Merge transcript TPMs from multiple quant.sf outputs:

taf-salmon salmon quantmerge \
  --quants sample1_quant sample2_quant \
  --names sample1 sample2 \
  --column TPM \
  -o merged_tpm.tsv

TAFFISH Command Mode

This is a normal TAFFISH tool app with command_mode = true.

For Salmon subcommands, prefer the explicit executable form:

taf-salmon salmon index ...
taf-salmon salmon quant ...
taf-salmon salmon quantmerge ...
taf-salmon salmon debug-map ...

Do not rely on:

taf-salmon index ...

In command mode, a non-option first argument can be interpreted as a container executable name rather than as a Salmon subcommand. The explicit taf-salmon salmon ... form is unambiguous and also lets users run the same container environment directly.

For option-leading arguments to the default upstream command, this also works:

taf-salmon -- --version
taf-salmon -- --help

Version Check And Network

Salmon 2 accepts --no-version-check and SALMON_NO_VERSION_CHECK for compatibility with C++ Salmon, but upstream documents them as no-ops: Salmon 2 does not contact the network for version checks. Keeping the flag in scripts is safe, but no longer necessary.

Functional Surface

Packaged upstream command:

• salmon index: build a Salmon 2 index from transcript FASTA
• salmon quant: quantify transcript abundance from reads or alignments
• salmon quant -a genome.bam --annotation genes.gtf: quantify from a name-grouped genome-aligned BAM plus annotation
• salmon quant --sketch: use the Salmon 2 sketch / pseudoalignment path
• salmon quant --decoder auto|serial|parallel|parallel=N: control compressed input decoding within the shared thread budget
• salmon quant --threadPolicy FILE: override the decoder engagement policy
• salmon quant --geneMap FILE: accept plain or compressed GTF/GFF/TSV gene maps
• salmon quant --writeRad: write RAD mappings while quantifying
• salmon quant --rad: quantify a RAD file directly
• salmon quant --fldPolicy baked|derive|prior: select the fragment-length distribution source for RAD quantification
• plain salmon quant: run deterministic two-phase quantification by default
• salmon quant --deterministic: accepted no-op compatibility spelling
• salmon quant --online: use the deprecated pre-2.6 one-pass path
• salmon quant --radScratchDir: relocate the temporary intermediate RAD
• salmon quant --radCompress lz4|zstd|none: select RAD compression
• salmon quant --skipQuant: stop after mapping and keep the output RAD
• salmon quant --writeBam: write unsorted BGZF BAM mappings
• salmon quant --writeSam: visible alias of the mapping SAM export
• salmon quant --bamCompressThreads: control BAM compression threads
• salmon quant --emAccel squarem|daarem: opt into EM/VBEM acceleration
• salmon quantmerge: merge Salmon quantification tables
• salmon debug-map: diagnostic per-read best-mapping detail
• salmon alevin: present only as an upstream migration message

Salmon 2 removed the legacy integrated salmon alevin implementation. This is an upstream change, not a TAFFISH packaging omission. Upstream recommends the piscem plus alevin-fry ecosystem for current single-cell workflows.

The old top-level salmon --cite command is not present in Salmon 2. Citation information remains documented upstream and below.

Compatibility Notes

Salmon 2.6.0 keeps index_version = 1 and requires no index rebuild from 2.5.1. Rebuild indices made by Salmon 2.0.x or older C++ / pufferfish versions.

Version 2.6.0 makes deterministic two-phase quantification the default for selective-alignment, sketch, and alignment input. aux_info/meta_info.json records inference_path as deterministic, online, or none; the last value is used for mapping-only --skipQuant. The default intermediate RAD is deleted on success. Upstream estimates temporary lz4 RAD usage at roughly 45 MB per million fragments in sketch mode and 55 MB per million fragments in selective alignment, with the exact size depending on multimapping.

The release also restores and corrects library-format accounting, removes decoy rows from RAD-based quant.sf, reports applied and detected library types separately, fixes metadata placeholders, and uses BAM AS tags by default in alignment mode. Pipelines that parse quant.sf by row number, interpret library_types as the detected type, or enforce thresholds on absolute compatible-fragment counts should review the upstream 2.6.0 migration notes.

Version 2.5.1 is a dependency and scheduler-hardening update. It replaces the adaptive mapping pool used in 2.5.0 with a fixed maximum worker set: workers above the current target park at batch boundaries and wake when the target grows, so no worker is created after startup and the configured ceiling is structural. Parked workers release record buffers. Upstream reports unchanged quantification results, identical mapped counts across modes, byte-identical serial/parallel quant.sf under --deterministic, and no index rebuild.

Version 2.5.0 makes -p a shared execution-slot budget for mapping and gzip decoding. It adds adaptive decoder scheduling, --decoder, --threadPolicy, content-based gzip/BGZF/bzip2/xz/zstd detection across input paths, and compressed --geneMap support. Upstream reports unchanged quantification results and no index rebuild requirement. It also fixes incomplete failed RAD outputs, widens packed equivalence-class offsets, improves gene-map validation and warnings, and updates the parallel decoding stack to include the upstream deadlock fix.

At a fixed thread count with the serial decoder, upstream reports byte-identical quant.sf output relative to 2.4.1. Across thread counts, floating-point shard reduction can vary below reported precision; repeated single-threaded runs are still expected to be byte-identical.

Version 2.4.1 fixed a RAD reader race introduced in 2.2.0. It could silently produce zero or partial counts in quant --rad, --deterministic, and genome projection with -a --annotation, especially at low thread counts. The runtime smoke retains repeated one-thread RAD regression coverage for this path.

Version 2.4.0 added:

• --writeBam FILE for unsorted BGZF BAM mapping export
• the visible --writeSam alias for --writeMappings
• --bamCompressThreads for BAM compression concurrency
• --fldPolicy baked|derive|prior for RAD fragment-length handling
• frag_length_source provenance in quantification metadata
• refreshed dependencies and security cleanup

Earlier Salmon 2 releases added sketch quantification, RAD separation, deterministic quantification, genome-projection quantification, SQUAREM/DAAREM acceleration, and the current index format. The migration guide documents old C++ options that were removed or retained only as no-ops. Integrated salmon alevin remains removed; use the alevin-fry ecosystem instead.

The app supports native Linux amd64 and native Linux arm64 through official upstream binaries. No Docker platform emulation is required for either declared platform.

The container includes the upstream binary, upstream README and BSD-3-Clause license, GNU runtime libraries, procps, and CA certificates. It does not bundle reference transcriptomes, genomes, decoy lists, annotation files, piscem, alevin-fry, simpleaf, oarfish, or external aligners.

Reference transcriptomes, genomes, decoy lists, annotations, reads, alignments, and RAD files are project-specific inputs rather than a fixed Salmon database. Salmon does not provide a production database downloader that should be mapped to a shared TAFFISH database path, so a database installation helper and automatic database mount are not applicable. Users mount or pass their own project inputs explicitly. The official 2.6.0 workspace and release assets provide the CLI only; no official local GUI, viewer extra, plugin GUI, or desktop companion is part of this app's upstream distribution.

Smoke Coverage

The smoke tests are independent and run without network access. They check:

• salmon 2.6.0 runtime version, embedded source identity, and top-level help
• no-op compatibility behavior for --no-version-check
• help for index, quant, quantmerge, and debug-map, including the sshashTmpDir, ramLimit, decoder, threadPolicy, writeRad, deterministic-default, online, radScratchDir, radCompress, skipQuant, errorModel, genome annotation, writeBam, writeSam, bamCompressThreads, fldPolicy, and emAccel
• dynamic library resolution through ldd
• a tiny Salmon 2 index build that writes info.json, index.ssi, and index.ctab, and records index_version = 1
• gzip-compressed single-end and paired-end selective-alignment quant runs with absolute processed, mapped, and NumReads mass assertions; the single-end case uses misleading filenames, an explicit serial decoder, a validated thread-policy JSON file, and a gzip-compressed gene map
• one single-thread and two eight-slot forced-parallel default quantifications; the smoke asserts the parallel execution plan, absolute processed/mapped counts, read-mass conservation, and byte-identical cross-thread/repeated quant.sf
• a tiny quant --sketch run that writes sketch_quant/quant.sf
• a transcriptome-SAM alignment-mode regression using U, SF, and SR, preserving the genuine single-end strandedness regression coverage
• genome-alignment projection from a tiny queryname-sorted SAM plus GTF, with absolute processed and mapped fragment assertions
• independent tiny --emAccel squarem and --emAccel daarem quantification
• real --writeBam and --writeSam exports, including BAM magic validation and BAM-input re-quantification
• eight low-thread RAD re-quantifications with absolute processed/mapped count assertions and frag_length_source = prior
• default deterministic, no-op --deterministic, deprecated --online, and conflicting-path behavior with exact inference_path assertions
• mapping-only --skipQuant with output-RAD retention and scratch cleanup
• zstd-compressed RAD writing followed by direct RAD quantification
• quantmerge on two synthetic quant.sf directories
• the upstream alevin removal and migration message

These tests verify packaging, command availability, and small real execution paths. They are not a substitute for biological validation on production references and read sets.

Upstream

• Upstream repository: https://github.com/COMBINE-lab/salmon
• Documentation: https://combine-lab.github.io/salmon/
• Release: https://github.com/COMBINE-lab/salmon/releases/tag/v2.6.0
• Release notes: https://github.com/COMBINE-lab/salmon/blob/v2.6.0/docs/release-notes-2.6.0.md
• Migration guide: https://github.com/COMBINE-lab/salmon/blob/v2.6.0/MIGRATION.md
• TAFFISH app packaging license: Apache-2.0
• Upstream license: BSD-3-Clause
• Citation: Patro et al. 2017, Nature Methods
• DOI: 10.1038/nmeth.4197
• PMID: 28263959