ehsanestaji · ehsanestaji · May 28, 2026 · May 28, 2026
diff --git a/README.md b/README.md
@@ -28,21 +28,39 @@ Run FastaGuard first.
 | Channel | Status |
 | --- | --- |
 | GitHub release | `v0.3.0` is live with Linux and macOS binaries |
-| Bioconda | `v0.2.0` is live; `v0.3.0` update is under Bioconda review |
-| BioContainers | `v0.2.0` is live; `v0.3.0` follows the Bioconda update |
+| Bioconda | `v0.3.0` is live for Linux and macOS x86_64/ARM64 |
+| BioContainers | `v0.3.0` is live as a pinned workflow image |
 | Source build | `v0.3.0` can be built from the Git tag |
 
 ## Install
 
-Latest release binary for Linux x86_64:
+Recommended bioinformatics install:
+
+```bash
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
+```
+
+Containerized workflow install:
+
+```bash
+docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
+```
+
+Run through BioContainers:
+
+```bash
+docker run --rm quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0 fastaguard --version
+```
+
+GitHub release binary for Linux x86_64:
 
 ```bash
 curl -L -O https://github.com/ehsanestaji/FastaGuard/releases/download/v0.3.0/fastaguard-v0.3.0-x86_64-unknown-linux-gnu.tar.gz
 tar -xzf fastaguard-v0.3.0-x86_64-unknown-linux-gnu.tar.gz
 ./fastaguard-v0.3.0-x86_64-unknown-linux-gnu/fastaguard --version
 ```
 
-Latest release binary for macOS Apple Silicon:
+GitHub release binary for macOS Apple Silicon:
 
 ```bash
 curl -L -O https://github.com/ehsanestaji/FastaGuard/releases/download/v0.3.0/fastaguard-v0.3.0-aarch64-apple-darwin.tar.gz
@@ -57,13 +75,6 @@ cargo install --git https://github.com/ehsanestaji/FastaGuard --tag v0.3.0
 fastaguard --version
 ```
 
-Bioconda install, currently serving the published `v0.2.0` package until the
-`v0.3.0` recipe update merges:
-
-```bash
-mamba install -c conda-forge -c bioconda fastaguard
-```
-
 Verify any installed CLI:
 
 ```bash
@@ -124,12 +135,10 @@ docker run --rm -v "$PWD:/data" fastaguard:local /data/sample.fa \
   --multiqc /data/fastaguard_mqc.json
 ```
 
-Published BioContainers currently provides the v0.2 image, which does not
-include v0.3 gate behavior yet. Use it for v0.2 workflows until the Bioconda
-v0.3 update propagates:
+Published BioContainers provides the v0.3 image for workflow engines:
 
 ```bash
-docker pull quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
 ```
 
 Exit codes:
@@ -244,7 +253,6 @@ FastaGuard catches FASTA-level assembly problems before expensive assembly QC.
 v0.3.0 is published on GitHub with Linux and macOS release binaries. It adds the
 assembly gate contract, checksum provenance, and evidence workflow.
 
-Bioconda currently serves v0.2.0 for `linux-64`, `linux-aarch64`, `osx-64`,
-and `osx-arm64`; the v0.3.0 Bioconda update is open and passing CI. The
-BioContainers v0.3 image will become available after the Bioconda package
-propagates.
+Bioconda serves v0.3.0 for `linux-64`, `linux-aarch64`, `osx-64`, and
+`osx-arm64`. BioContainers publishes the pinned v0.3 workflow image
+`quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0`.
diff --git a/docs/adoption-plan.md b/docs/adoption-plan.md
@@ -15,9 +15,9 @@ Bioconda published -> BioContainers available -> MultiQC plugin -> public benchm
 
 Goal: make installation natural for bioinformatics users.
 
-Status: Bioconda is live for FastaGuard v0.2.0 on Linux and macOS x86_64/ARM64
+Status: Bioconda is live for FastaGuard v0.3.0 on Linux and macOS x86_64/ARM64
 platforms. BioContainers publishes the pinned workflow image
-`quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0`.
+`quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0`.
 
 - Keep GitHub release binaries working.
 - Keep Docker smoke tests passing.
@@ -27,7 +27,7 @@ platforms. BioContainers publishes the pinned workflow image
 Done when:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
 fastaguard --schema
 ```
 

diff --git a/docs/benchmarking.md b/docs/benchmarking.md
@@ -87,11 +87,11 @@ Use it to answer:
 
 Do not use it to claim performance on contaminated assemblies, highly ambiguous assemblies, or compressed FASTA until separate fixtures cover those cases.
 
-## v0.2 Evidence Targets
+## Evidence Targets
 
 FastaGuard should prove four preflight categories with small reproducible
-fixtures. For v0.3, the same evidence should also show whether each category
-blocks the pipeline gate:
+fixtures. For v0.3, the evidence should also show whether each category blocks
+the pipeline gate:
 
 | Evidence case | Gate behavior | What FastaGuard catches | Why it should run before heavier tools |
 | --- | --- | --- | --- |
@@ -132,10 +132,9 @@ This evidence matters more than synthetic speed alone because it shows the wedge
 
 ## Evidence Pack Workflow
 
-The v0.2 evidence workflow is documented in
-`docs/evidence/fastaguard-v0.2-evidence.md`.
-The published evidence document remains v0.2-focused; v0.3 gate evidence should
-extend that workflow after the gate contract is released.
+The original v0.2 evidence workflow is documented in
+`docs/evidence/fastaguard-v0.2-evidence.md`. The v0.3 gate evidence workflow is
+documented in `docs/evidence/fastaguard-v0.3-evidence.md`.
 
 CI-safe local run:
 
@@ -151,7 +150,7 @@ Public NCBI run:
 ```bash
 python3 scripts/collect_evidence.py \
   --binary target/release/fastaguard \
-  --out-dir target/evidence/v0.2
+  --out-dir target/evidence/v0.3
 ```
 
 The public run uses NCBI Datasets commands such as

diff --git a/docs/packaging.md b/docs/packaging.md
@@ -5,26 +5,26 @@
 Treat packaging as part of the product, not as a later chore. For bioinformatics adoption, the order should be:
 
 ```text
-Bioconda -> GitHub release binaries -> Docker image -> BioContainers -> Homebrew later
+Bioconda -> BioContainers -> GitHub release binaries -> Docker image -> Homebrew later
 ```
 
-FastaGuard v0.2.0 is published on GitHub with Linux and macOS release binaries.
-Bioconda serves v0.2.0 on Linux and macOS x86_64/ARM64 platforms. Docker remains
-useful for local smoke tests, while BioContainers now provides the pinned
-workflow image generated from the Bioconda package.
+FastaGuard v0.3.0 is published on GitHub with Linux and macOS release binaries.
+Bioconda serves v0.3.0 on Linux and macOS x86_64/ARM64 platforms.
+BioContainers provides the pinned v0.3 workflow image generated from the
+Bioconda package. Docker remains useful for local smoke tests.
 
 ## Bioconda
 
 Recommended install:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
 ```
 
 Conda equivalent:
 
 ```bash
-conda install -c conda-forge -c bioconda fastaguard
+conda install -c conda-forge -c bioconda fastaguard=0.3.0
 ```
 
 Verify the installed package:
@@ -37,7 +37,7 @@ fastaguard --finding-catalog
 
 Current published package:
 
-- Version: `0.2.0`
+- Version: `0.3.0`
 - Platforms: `linux-64`, `linux-aarch64`, `osx-64`, `osx-arm64`
 - Package page: [anaconda.org/bioconda/fastaguard](https://anaconda.org/bioconda/fastaguard)
 
@@ -89,8 +89,8 @@ For a public release:
 1. Tag the release:
 
    ```bash
-   git tag v0.2.0
-   git push origin v0.2.0
+   git tag v0.3.0
+   git push origin v0.3.0
    ```
 
 2. Push the tag to trigger `.github/workflows/release.yml`.
@@ -144,7 +144,7 @@ The Bioconda recipe has merged upstream and generated a BioContainers image.
 Use the pinned tag in workflow examples:
 
 ```bash
-docker pull quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
 ```
 
 That path is preferable to maintaining a separate BioContainers Dockerfile.

diff --git a/docs/releases/v0.3.0.md b/docs/releases/v0.3.0.md
@@ -23,15 +23,26 @@ or other expensive downstream QC.
 
 ## Install
 
-Download the platform binary from this GitHub release, or build from source:
+Install through Bioconda:
 
 ```bash
-cargo install --git https://github.com/ehsanestaji/FastaGuard --tag v0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
 fastaguard --version
 ```
 
-Bioconda and BioContainers updates should follow after the v0.3.0 source
-archive and release assets are public.
+Run the pinned BioContainers image:
+
+```bash
+docker run --rm quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0 fastaguard --version
+```
+
+You can also download a platform binary from this GitHub release, or build from
+source:
+
+```bash
+cargo install --git https://github.com/ehsanestaji/FastaGuard --tag v0.3.0
+fastaguard --version
+```
 
 ## Pipeline Gate
 

diff --git a/docs/roadmap.md b/docs/roadmap.md
@@ -60,8 +60,7 @@ Make FastaGuard credible enough for pipeline authors to add as a default assembl
 Development scope:
 
 - public evidence pack from local fixtures and public assemblies
-- Bioconda and BioContainers v0.2 availability documented without implying a
-  v0.3 package exists yet
+- Bioconda and BioContainers v0.3 availability documented as live
 - input checksum provenance with `provenance.input_sha256`
 - clearer machine-readable threshold metadata
 - assembly gate preset with `--gate pipeline`

diff --git a/docs/tool-landscape.md b/docs/tool-landscape.md
@@ -56,12 +56,12 @@ Current product evidence:
 - Rust CLI builds and runs as a single binary.
 - Docker build and smoke test pass.
 - GitHub release workflow builds Linux and macOS binaries.
-- FastaGuard v0.2.0 is published on GitHub with Linux and macOS binaries.
-- FastaGuard v0.2.0 is published on Bioconda for `linux-64`,
+- FastaGuard v0.3.0 is published on GitHub with Linux and macOS binaries.
+- FastaGuard v0.3.0 is published on Bioconda for `linux-64`,
   `linux-aarch64`, `osx-64`, and `osx-arm64`.
 - Clean Bioconda install has been smoke-tested with `fastaguard --schema`.
 - BioContainers publishes
-  `quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0`.
+  `quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0`.
 - JSON Schema validates committed golden reports.
 - Reports include bounded evidence records and suggested actions.
 - The v0.3 gate contract exposes `gate.blocking_findings`,
@@ -72,11 +72,12 @@ Current product evidence:
 - nf-core, Nextflow, and Snakemake starters exist under `examples/`.
 - The v0.2 evidence workflow is documented in
   `docs/evidence/fastaguard-v0.2-evidence.md`.
+- The v0.3 gate evidence workflow is documented in
+  `docs/evidence/fastaguard-v0.3-evidence.md`.
 
 Evidence still needed:
 
 - committed benchmark summaries from public assemblies
-- v0.3 assembly gate evidence runs using `--gate pipeline`
 - user feedback from real pipeline authors
 - broader public assembly evidence runs
 - official MultiQC module or packaged plugin

diff --git a/docs/vision-plan.md b/docs/vision-plan.md
@@ -48,7 +48,7 @@ Make FastaGuard credible enough for pipeline authors to add as a default assembl
 Priorities:
 
 - publish a small evidence pack from local fixtures and public assemblies
-- document Bioconda and BioContainers v0.2 availability
+- document Bioconda and BioContainers v0.3 availability
 - add input checksums to provenance
 - add clearer machine-readable threshold metadata
 - add an assembly gate preset for common pipeline behavior

diff --git a/examples/nf-core/README.md b/examples/nf-core/README.md
@@ -20,19 +20,15 @@ The module assumes `fastaguard` is available on `PATH` when run without a
 container. The recommended install is:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
 ```
 
-Published BioContainers currently provides the v0.2 image:
+Published BioContainers provides the pinned v0.3 image:
 
 ```text
-quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
 ```
 
-Do not pair that v0.2 image with the v0.3 `--gate pipeline` command below.
-Run this starter with a current local v0.3 binary, or add a v0.3 container tag
-after the v0.3 BioContainers image is available.
-
 The command block is written for the v0.3 assembly gate and runs:
 
 ```bash

diff --git a/examples/nf-core/modules/local/fastaguard/main.nf b/examples/nf-core/modules/local/fastaguard/main.nf
@@ -1,6 +1,7 @@
 process FASTAGUARD {
     tag "$meta.id"
     label 'process_low'
+    container 'quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0'
 
     input:
     tuple val(meta), path(fasta)

diff --git a/examples/snakemake/wrapper/README.md b/examples/snakemake/wrapper/README.md
@@ -2,15 +2,12 @@
 
 This is a local wrapper-style starter for FastaGuard. It assumes `fastaguard` is available on `PATH`.
 
-Published Bioconda currently provides v0.2.0:
+Published Bioconda provides v0.3.0:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
 ```
 
-The v0.3 gate example below needs a current local v0.3 binary until the v0.3
-Bioconda package is published.
-
 Run from this directory with a `sample.fa` input:
 
 ```bash
@@ -27,23 +24,18 @@ That gate blocks downstream workflow steps on duplicate IDs, invalid characters,
 invalid FASTA structure, and high-N content. GC and length outliers remain
 advisory unless explicitly added with `--fail-on`. Gate failures intentionally exit with code `2` after writing reports, so downstream workflow steps stop while the JSON/HTML evidence remains available.
 
-The wrapper also includes a v0.3 Conda environment for use after the v0.3
-Bioconda package is published:
+The wrapper also includes a v0.3 Conda environment:
 
 ```bash
 snakemake -s Snakefile --cores 1 --use-conda
 ```
 
-For current published containerized workflow runs, the latest pinned
-BioContainers image is still v0.2:
+For containerized workflow runs, the latest pinned BioContainers image is:
 
 ```text
-quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
 ```
 
-Do not pair that v0.2 image with `--gate pipeline`; update the container tag
-when a v0.3 BioContainers image is available for gate runs.
-
 The wrapper emits:
 
 - `fastaguard_report.html`

diff --git a/packaging/bioconda/README.md b/packaging/bioconda/README.md
@@ -1,23 +1,23 @@
 # Bioconda Recipe
 
-Upstream Bioconda currently publishes FastaGuard v0.2.0.
+Upstream Bioconda currently publishes FastaGuard v0.3.0.
 
 The recipe has been merged into `bioconda/bioconda-recipes` as
 `recipes/fastaguard/`, and the current published package is available from
 Bioconda:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard
+mamba install -c conda-forge -c bioconda fastaguard=0.3.0
 ```
 
 BioContainers publishes the pinned workflow image:
 
 ```bash
-docker pull quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
 ```
 
-This local recipe directory mirrors the FastaGuard v0.2.0 Bioconda recipe. The
-v0.2.0 GitHub source archive is published and `meta.yaml` includes the real
+This local recipe directory mirrors the FastaGuard v0.3.0 Bioconda recipe. The
+v0.3.0 GitHub source archive is published and `meta.yaml` includes the real
 archive SHA256.
 
 ## Local Checks