ehsanestaji · ehsanestaji · Jul 3, 2026 · Jul 3, 2026
diff --git a/README.md b/README.md
@@ -49,52 +49,52 @@ downstream tool.
 
 | Channel | Status |
 | --- | --- |
-| Source/package metadata | this branch/package metadata targets `v0.5.0`; `v0.4.0` is the latest tagged source release |
-| GitHub release | v0.4 GitHub release binaries are built from the `v0.4.0` tag |
-| Bioconda | `v0.3.0` is live for Linux and macOS x86_64/ARM64; v0.5 is not yet published there |
-| BioContainers | `v0.3.0` is live as a pinned workflow image; v0.5 is not yet published there |
+| Source/package metadata | `v0.5.0` is the latest tagged source release |
+| GitHub release | v0.5 GitHub release binaries are built from the `v0.5.0` tag |
+| Bioconda | `v0.5.0` is live for Linux and macOS x86_64/ARM64 |
+| BioContainers | `v0.5.0` is live as a pinned workflow image |
 | Source build | local checkout builds report the package version from `Cargo.toml` |
 
 ## Install
 
 Published bioinformatics install:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard=0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.5.0
 ```
 
 Published containerized workflow install:
 
 ```bash
-docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
 Run through BioContainers:
 
 ```bash
-docker run --rm quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0 fastaguard --version
+docker run --rm quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0 fastaguard --version
 ```
 
 GitHub release binary for Linux x86_64:
 
 ```bash
-curl -L -O https://github.com/ehsanestaji/FastaGuard/releases/download/v0.4.0/fastaguard-v0.4.0-x86_64-unknown-linux-gnu.tar.gz
-tar -xzf fastaguard-v0.4.0-x86_64-unknown-linux-gnu.tar.gz
-./fastaguard-v0.4.0-x86_64-unknown-linux-gnu/fastaguard --version
+curl -L -O https://github.com/ehsanestaji/FastaGuard/releases/download/v0.5.0/fastaguard-v0.5.0-x86_64-unknown-linux-gnu.tar.gz
+tar -xzf fastaguard-v0.5.0-x86_64-unknown-linux-gnu.tar.gz
+./fastaguard-v0.5.0-x86_64-unknown-linux-gnu/fastaguard --version
 ```
 
 GitHub release binary for macOS Apple Silicon:
 
 ```bash
-curl -L -O https://github.com/ehsanestaji/FastaGuard/releases/download/v0.4.0/fastaguard-v0.4.0-aarch64-apple-darwin.tar.gz
-tar -xzf fastaguard-v0.4.0-aarch64-apple-darwin.tar.gz
-./fastaguard-v0.4.0-aarch64-apple-darwin/fastaguard --version
+curl -L -O https://github.com/ehsanestaji/FastaGuard/releases/download/v0.5.0/fastaguard-v0.5.0-aarch64-apple-darwin.tar.gz
+tar -xzf fastaguard-v0.5.0-aarch64-apple-darwin.tar.gz
+./fastaguard-v0.5.0-aarch64-apple-darwin/fastaguard --version
 ```
 
 Build from the latest published Git tag:
 
 ```bash
-cargo install --git https://github.com/ehsanestaji/FastaGuard --tag v0.4.0
+cargo install --git https://github.com/ehsanestaji/FastaGuard --tag v0.5.0
 fastaguard --version
 ```
 
@@ -122,7 +122,7 @@ fastaguard --version
 
 The `--gate pipeline` examples below require FastaGuard `v0.3.0` or newer.
 The `fastaguard compare` example requires FastaGuard `v0.4.0` or newer.
-The `--gate submission` example requires the v0.5 source/package contract.
+The `--gate submission` example requires FastaGuard `v0.5.0` or newer.
 
 Run the assembly preflight check:
 
@@ -153,8 +153,8 @@ v0.4 compare starter example:
 fastaguard compare assemblies/*.fa --profile assembly --gate pipeline
 ```
 
-This command is part of the v0.4 GitHub release. Bioconda and BioContainers may
-still be `v0.3.0` until packaging publication follow-up is complete.
+This command first shipped in the v0.4 GitHub release and is included in the
+published v0.5.0 Bioconda package and BioContainers image.
 
 Submission-readiness preflight:
 
@@ -191,10 +191,10 @@ docker run --rm -v "$PWD:/data" fastaguard:local /data/sample.fa \
   --multiqc /data/fastaguard_mqc.json
 ```
 
-Published BioContainers provides the v0.3 image for workflow engines:
+Published BioContainers provides the v0.5 image for workflow engines:
 
 ```bash
-docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
 Exit codes:
@@ -333,13 +333,10 @@ FastaGuard catches FASTA-level assembly problems before expensive assembly QC.
 
 ## Status
 
-This branch/package metadata targets FastaGuard v0.5.0. The latest tagged
-GitHub release remains v0.4.0, which adds preflight readiness, compare mode,
-and cohort-level FASTA triage outputs.
+FastaGuard v0.5.0 is the latest tagged GitHub release and the current published
+Bioconda/BioContainers release. It adds the submission-readiness gate on top of
+the v0.4 preflight readiness and compare-mode contract.
 
-v0.3.0 remains the current Bioconda and BioContainers release until packaging
-follow-up is complete.
-
-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`.
+Bioconda serves v0.5.0 for `linux-64`, `linux-aarch64`, `osx-64`, and
+`osx-arm64`. BioContainers publishes the pinned v0.5 workflow image
+`quay.io/biocontainers/fastaguard:0.5.0--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 v0.3.0 on Linux and macOS x86_64/ARM64
+Status: Bioconda is live for FastaGuard v0.5.0 on Linux and macOS x86_64/ARM64
 platforms. BioContainers publishes the pinned workflow image
-`quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0`.
+`quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0`.
 
 - Keep GitHub release binaries working.
 - Keep Docker smoke tests passing.
@@ -27,12 +27,13 @@ platforms. BioContainers publishes the pinned workflow image
 Done when:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard=0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.5.0
 fastaguard --schema
 ```
 
 works in a clean environment, and workflow engines can pull the pinned
-BioContainers image.
+BioContainers image. This is now true for v0.5.0; keep repeating the same
+check for future releases.
 
 ## Phase 2: Aggregate
 

diff --git a/docs/packaging.md b/docs/packaging.md
@@ -8,28 +8,27 @@ Treat packaging as part of the product, not as a later chore. For bioinformatics
 Bioconda -> BioContainers -> GitHub release binaries -> Docker image -> Homebrew later
 ```
 
-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
+FastaGuard v0.5.0 is published on GitHub with Linux and macOS release binaries.
+Bioconda serves v0.5.0 on Linux and macOS x86_64/ARM64 platforms.
+BioContainers provides the pinned v0.5 workflow image generated from the
 Bioconda package. Docker remains useful for local smoke tests.
 
-This branch/package metadata targets v0.5.0, including the
-`--gate submission` and `--submission-target generic|ncbi` contract. Do not
-document v0.5 as published on Bioconda or BioContainers until those packages
-exist; the verified published package and workflow image remain v0.3.0.
+The current published package includes the `--gate submission` and
+`--submission-target generic|ncbi` contract. Keep future docs pinned to
+confirmed Bioconda and BioContainers versions before advertising them as live.
 
 ## Bioconda
 
 Recommended install:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard=0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.5.0
 ```
 
 Conda equivalent:
 
 ```bash
-conda install -c conda-forge -c bioconda fastaguard=0.3.0
+conda install -c conda-forge -c bioconda fastaguard=0.5.0
 ```
 
 Verify the installed package:
@@ -42,7 +41,7 @@ fastaguard --finding-catalog
 
 Current published package:
 
-- Version: `0.3.0`
+- Version: `0.5.0`
 - Platforms: `linux-64`, `linux-aarch64`, `osx-64`, `osx-arm64`
 - Package page: [anaconda.org/bioconda/fastaguard](https://anaconda.org/bioconda/fastaguard)
 
@@ -105,8 +104,8 @@ For a public release:
 1. Tag the release:
 
    ```bash
-   git tag v0.3.0
-   git push origin v0.3.0
+   git tag v0.5.0
+   git push origin v0.5.0
    ```
 
 2. Push the tag to trigger `.github/workflows/release.yml`.
@@ -160,7 +159,7 @@ 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:0.3.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
 That path is preferable to maintaining a separate BioContainers Dockerfile.

diff --git a/docs/tool-landscape.md b/docs/tool-landscape.md
@@ -81,12 +81,12 @@ 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 v0.3.0 is published on GitHub with Linux and macOS binaries.
-- FastaGuard v0.3.0 is published on Bioconda for `linux-64`,
+- FastaGuard v0.5.0 is published on GitHub with Linux and macOS binaries.
+- FastaGuard v0.5.0 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:0.3.0--hfa8f182_0`.
+  `quay.io/biocontainers/fastaguard:0.5.0--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`,

diff --git a/examples/nf-core/README.md b/examples/nf-core/README.md
@@ -20,13 +20,13 @@ 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=0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.5.0
 ```
 
-Published BioContainers provides the pinned v0.3 image:
+Published BioContainers provides the pinned v0.5 image:
 
 ```text
-quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
+quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
 The command block is written for the v0.3 assembly gate and runs:
@@ -50,7 +50,7 @@ fastaguard compare assemblies/*.fa --profile assembly --gate pipeline
 ```
 
 For v0.5 submission-readiness preflight before official validators, use the
-source/package contract rather than the currently published v0.3 container:
+published v0.5 package or container:
 
 ```bash
 fastaguard {input.fasta} --gate submission --submission-target ncbi

diff --git a/examples/nf-core/modules/local/fastaguard/main.nf b/examples/nf-core/modules/local/fastaguard/main.nf
@@ -1,7 +1,7 @@
 process FASTAGUARD {
     tag "$meta.id"
     label 'process_low'
-    container 'quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0'
+    container 'quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0'
 
     input:
     tuple val(meta), path(fasta)

diff --git a/examples/snakemake/wrapper/README.md b/examples/snakemake/wrapper/README.md
@@ -2,10 +2,10 @@
 
 This is a local wrapper-style starter for FastaGuard. It assumes `fastaguard` is available on `PATH`.
 
-Published Bioconda provides v0.3.0:
+Published Bioconda provides v0.5.0:
 
 ```bash
-mamba install -c conda-forge -c bioconda fastaguard=0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.5.0
 ```
 
 Run from this directory with a `sample.fa` input:
@@ -24,15 +24,14 @@ 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:
+The wrapper also includes a v0.5 Conda environment:
 
 ```bash
 snakemake -s Snakefile --cores 1 --use-conda
 ```
 
 For v0.5 submission-readiness preflight before official validators, use the
-source/package contract rather than the currently published v0.3 package or
-container:
+published v0.5 package or container:
 
 ```bash
 fastaguard {input.fasta} --gate submission --submission-target ncbi
@@ -48,7 +47,7 @@ Pipeline authors should route on:
 For containerized workflow runs, the latest pinned BioContainers image is:
 
 ```text
-quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
+quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
 The wrapper emits:

diff --git a/examples/snakemake/wrapper/environment.yaml b/examples/snakemake/wrapper/environment.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - fastaguard=0.3.0
+  - fastaguard=0.5.0
diff --git a/packaging/bioconda/README.md b/packaging/bioconda/README.md
@@ -1,23 +1,23 @@
 # Bioconda Recipe
 
-Upstream Bioconda currently publishes FastaGuard v0.3.0.
+Upstream Bioconda currently publishes FastaGuard v0.5.0.
 
 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=0.3.0
+mamba install -c conda-forge -c bioconda fastaguard=0.5.0
 ```
 
 BioContainers publishes the pinned workflow image:
 
 ```bash
-docker pull quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0
+docker pull quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0
 ```
 
-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
+This local recipe directory mirrors the FastaGuard v0.5.0 Bioconda recipe. The
+v0.5.0 GitHub source archive is published and `meta.yaml` includes the real
 archive SHA256.
 
 ## Local Checks

diff --git a/packaging/bioconda/meta.yaml b/packaging/bioconda/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "fastaguard" %}
-{% set version = "0.3.0" %}
+{% set version = "0.5.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/ehsanestaji/FastaGuard/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 643d5d0107b6dc237f3be782a8463414880b95c45964397b773dac7e794e4fde
+  sha256: b3de60c83cb570bb90e894c262effe4092101b1655e5c64023445078ee2c5971
 
 build:
   number: 0

diff --git a/tests/python/test_adoption_assets.py b/tests/python/test_adoption_assets.py
@@ -79,7 +79,7 @@ def test_v0_3_gate_examples_do_not_pin_v0_2_runtimes(self):
 
         self.assertNotIn("0.2.0--", nf_core_module)
         self.assertIn(
-            "quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0",
+            "quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0",
             nf_core_module,
         )
         self.assertNotIn("fastaguard=0.2.0", wrapper_env)
@@ -488,12 +488,12 @@ def test_workflow_docs_reference_bioconda_and_container_status(self):
         self.assertIn(install, nfcore_readme)
         self.assertIn(install, snakemake_readme)
         self.assertIn(
-            "quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0",
+            "quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0",
             nfcore_readme,
         )
         self.assertNotIn("0.2.0--", nfcore_module)
         self.assertIn(
-            "quay.io/biocontainers/fastaguard:0.3.0--hfa8f182_0",
+            "quay.io/biocontainers/fastaguard:0.5.0--hfa8f182_0",
             snakemake_readme,
         )
 
@@ -825,7 +825,7 @@ def test_snakemake_wrapper_declares_bioconda_environment(self):
                 "  - conda-forge",
                 "  - bioconda",
                 "dependencies:",
-                "  - fastaguard=0.3.0",
+                "  - fastaguard=0.5.0",
             ],
         )
         self.assertIn('conda: "environment.yaml"', snakefile.read_text())