AustralianBioCommons · amandazhuyilan · Jul 2, 2026
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,20 +1,20 @@
-# ziadbkh/bindflow: Contributing Guidelines
+# AustralianBioCommons/sbp-bindflow: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving ziadbkh/bindflow.
+Many thanks for taking an interest in improving AustralianBioCommons/sbp-bindflow.
 
-We try to manage the required tasks for ziadbkh/bindflow using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for AustralianBioCommons/sbp-bindflow using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for ziadbkh/bindflow, the standard workflow is as follows:
+If you'd like to write some code for AustralianBioCommons/sbp-bindflow, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [ziadbkh/bindflow issues](https://github.com/ziadbkh/bindflow/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [ziadbkh/bindflow repository](https://github.com/ziadbkh/bindflow) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [AustralianBioCommons/sbp-bindflow issues](https://github.com/AustralianBioCommons/sbp-bindflow/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [AustralianBioCommons/sbp-bindflow repository](https://github.com/AustralianBioCommons/sbp-bindflow) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -58,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the ziadbkh/bindflow code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the AustralianBioCommons/sbp-bindflow code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -40,4 +40,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of ziadbkh/bindflow _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of AustralianBioCommons/sbp-bindflow _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the ziadbkh/bindflow pipeline
+description: Suggest an idea for the AustralianBioCommons/sbp-bindflow pipeline
 labels: enhancement
 body:
   - type: textarea

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,21 +1,21 @@
 <!--
-# ziadbkh/bindflow pull request
+# AustralianBioCommons/sbp-bindflow pull request
 
-Many thanks for contributing to ziadbkh/bindflow!
+Many thanks for contributing to AustralianBioCommons/sbp-bindflow!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/ziadbkh/bindflow/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/AustralianBioCommons/sbp-bindflow/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/ziadbkh/bindflow/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/AustralianBioCommons/sbp-bindflow/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'ziadbkh/bindflow'
+        if: github.repository == 'AustralianBioCommons/sbp-bindflow'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == ziadbkh/bindflow ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == AustralianBioCommons/sbp-bindflow ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'ziadbkh/bindflow') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'AustralianBioCommons/sbp-bindflow') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'ziadbkh/bindflow'
+      github.repository == 'AustralianBioCommons/sbp-bindflow'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/ziadbkh/bindflow/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/AustralianBioCommons/sbp-bindflow/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -42,7 +42,7 @@ template:
   force: true
   is_nfcore: false
   name: bindflow
-  org: ziadbkh
+  org: AustralianBioCommons
   outdir: .
   skip_features:
   - igenomes

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,14 +1,14 @@
-# Australian-Structural-Biology-Computing/bindflow: Changelog
+# AustralianBioCommons/sbp-bindflow: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## v1.0.0dev - [date]
 
-Initial release of Australian-Structural-Biology-Computing/bindflow, created with the [nf-core](https://nf-co.re/) template.
+Initial release of AustralianBioCommons/sbp-bindflow, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
-- [[#PR1](https://github.com/Australian-Structural-Biology-Computing/bindflow/pull/1)] - Add basic workflow documentation.
+- [[#PR1](https://github.com/AustralianBioCommons/sbp-bindflow/pull/1)] - Add basic workflow documentation.
 
 ### `Fixed`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,4 +1,4 @@
-# Australian-Structural-Biology-Computing/bindflow: Citations
+# AustralianBioCommons/sbp-bindflow: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

diff --git a/README.md b/README.md
@@ -1,20 +1,20 @@
 
 
-# Australian-Structural-Biology-Computing/bindflow
+# AustralianBioCommons/sbp-bindflow
 
-[![GitHub Actions CI Status](https://github.com/Australian-Structural-Biology-Computing/bindflow/actions/workflows/ci.yml/badge.svg)](https://github.com/Australian-Structural-Biology-Computing/bindflow/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/Australian-Structural-Biology-Computing/bindflow/actions/workflows/linting.yml/badge.svg)](https://github.com/Australian-Structural-Biology-Computing/bindflow/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions CI Status](https://github.com/AustralianBioCommons/sbp-bindflow/actions/workflows/ci.yml/badge.svg)](https://github.com/AustralianBioCommons/sbp-bindflow/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/AustralianBioCommons/sbp-bindflow/actions/workflows/linting.yml/badge.svg)](https://github.com/AustralianBioCommons/sbp-bindflow/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/Australian-Structural-Biology-Computing/bindflow)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/AustralianBioCommons/sbp-bindflow)
 
 ## Introduction
 
-**Australian-Structural-Biology-Computing/bindflow** is a bioinformatics pipeline that generates protein binders for user-defined hotspot residues on a target protein structure.
+**AustralianBioCommons/sbp-bindflow** is a bioinformatics pipeline that generates protein binders for user-defined hotspot residues on a target protein structure.
 The pipeline will be executed until a user-defined number of designs pass the in-silico quality control criteria.
 
 <!-- TODO nf-core:
@@ -86,7 +86,7 @@ Now, you can run the pipeline using:
 <!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
 
 ```bash
-nextflow run Australian-Structural-Biology-Computing/bindflow \
+nextflow run AustralianBioCommons/sbp-bindflow \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
@@ -98,7 +98,7 @@ nextflow run Australian-Structural-Biology-Computing/bindflow \
 
 ## Credits
 
-Australian-Structural-Biology-Computing/bindflow was originally written by Ziad Al-Bkhetan and Thomas Litfin.
+AustralianBioCommons/sbp-bindflow was originally written by Ziad Al-Bkhetan and Thomas Litfin.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -111,7 +111,7 @@ If you would like to contribute to this pipeline, please see the [contributing g
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use Australian-Structural-Biology-Computing/bindflow for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use AustralianBioCommons/sbp-bindflow for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 

diff --git a/assets/email_template.html b/assets/email_template.html
@@ -4,21 +4,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="ziadbkh/bindflow: bindcraft and others">
-  <title>ziadbkh/bindflow Pipeline Report</title>
+  <meta name="description" content="AustralianBioCommons/sbp-bindflow: bindcraft and others">
+  <title>AustralianBioCommons/sbp-bindflow Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>ziadbkh/bindflow ${version}</h1>
+<h1>AustralianBioCommons/sbp-bindflow ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">ziadbkh/bindflow execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">AustralianBioCommons/sbp-bindflow execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -27,7 +27,7 @@ <h4 style="margin-top:0; color: inherit;">ziadbkh/bindflow execution completed u
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        ziadbkh/bindflow execution completed successfully!
+        AustralianBioCommons/sbp-bindflow execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>ziadbkh/bindflow</p>
-<p><a href="https://github.com/ziadbkh/bindflow">https://github.com/ziadbkh/bindflow</a></p>
+<p>AustralianBioCommons/sbp-bindflow</p>
+<p><a href="https://github.com/AustralianBioCommons/sbp-bindflow">https://github.com/AustralianBioCommons/sbp-bindflow</a></p>
 
 </div>
 

diff --git a/assets/email_template.txt b/assets/email_template.txt
@@ -1,10 +1,10 @@
 Run Name: $runName
 
 <% if (success){
-    out << "## ziadbkh/bindflow execution completed successfully! ##"
+    out << "## AustralianBioCommons/sbp-bindflow execution completed successfully! ##"
 } else {
     out << """####################################################
-## ziadbkh/bindflow execution completed unsuccessfully! ##
+## AustralianBioCommons/sbp-bindflow execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -27,5 +27,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-ziadbkh/bindflow
-https://github.com/ziadbkh/bindflow
+AustralianBioCommons/sbp-bindflow
+https://github.com/AustralianBioCommons/sbp-bindflow
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
@@ -1,13 +1,13 @@
 id: "ziadbkh-bindflow-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "ziadbkh/bindflow Methods Description"
-section_href: "https://github.com/ziadbkh/bindflow"
+section_name: "AustralianBioCommons/sbp-bindflow Methods Description"
+section_href: "https://github.com/AustralianBioCommons/sbp-bindflow"
 plot_type: "html"
 ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using ziadbkh/bindflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using AustralianBioCommons/sbp-bindflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/ziadbkh/bindflow/tree/dev" target="_blank">ziadbkh/bindflow</a>
+  This report has been generated by the <a href="https://github.com/AustralianBioCommons/sbp-bindflow/tree/dev" target="_blank">AustralianBioCommons/sbp-bindflow</a>
   analysis pipeline.
 report_section_order:
   "ziadbkh-bindflow-methods-description":

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,2 +1,2 @@
 id,binder_name,starting_pdb,chains,target_hotspot_residues,min_length,max_length,number_of_final_designs,settings_filters,settings_advanced
-s1,PDL1,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/PDL1.pdb,A,56,65,150,4,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/default_filters.json,https://raw.githubusercontent.com/Australian-Structural-Biology-Computing/bindflow/refs/heads/main/assets/bindcraft/default_4stage_multimer.json
+s1,PDL1,https://raw.githubusercontent.com/AustralianBioCommons/sbp-bindflow/refs/heads/main/assets/bindcraft/PDL1.pdb,A,56,65,150,4,https://raw.githubusercontent.com/AustralianBioCommons/sbp-bindflow/refs/heads/main/assets/bindcraft/default_filters.json,https://raw.githubusercontent.com/AustralianBioCommons/sbp-bindflow/refs/heads/main/assets/bindcraft/default_4stage_multimer.json
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -1,7 +1,7 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/ziadbkh/bindflow/master/assets/schema_input.json",
-    "title": "ziadbkh/bindflow pipeline - params.input schema",
+    "$id": "https://raw.githubusercontent.com/AustralianBioCommons/sbp-bindflow/master/assets/schema_input.json",
+    "title": "AustralianBioCommons/sbp-bindflow pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {

diff --git a/conf/base.config b/conf/base.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    ziadbkh/bindflow Nextflow base config file
+    AustralianBioCommons/sbp-bindflow Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on