diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index eb2d1d8..0910078 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,9 +1,9 @@ -# 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! @@ -11,10 +11,10 @@ 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 index da0f488..8cb2fe7 100644 --- 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 index b0b3795..3d072a8 100644 --- 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 index 1e3dd28..f4ac723 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,21 +1,21 @@ ## 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 `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 23ab09a..d9fa70e 100644 --- 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" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5f346a5..5cabd0b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,7 +22,7 @@ jobs: test: name: "Run pipeline with test data (${{ 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 index a4bc945..ee763c5 100644 --- 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 index f58e338..8bbf2d1 100644 --- 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 index 95f59f2..2750eaa 100644 --- 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 index 0622cbb..4ab9a48 100644 --- 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 index c78da61..6a4c685 100644 --- 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. ```bash -nextflow run Australian-Structural-Biology-Computing/bindflow \ +nextflow run AustralianBioCommons/sbp-bindflow \ -profile \ --input samplesheet.csv \ --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 - + diff --git a/assets/email_template.html b/assets/email_template.html index 4df8357..22f4614 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,21 +4,21 @@ - - ziadbkh/bindflow Pipeline Report + + AustralianBioCommons/sbp-bindflow Pipeline Report
-

ziadbkh/bindflow ${version}

+

AustralianBioCommons/sbp-bindflow ${version}

Run Name: $runName

<% if (!success){ 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:

${errorReport}
@@ -27,7 +27,7 @@

ziadbkh/bindflow execution completed u } else { out << """
- ziadbkh/bindflow execution completed successfully! + AustralianBioCommons/sbp-bindflow execution completed successfully!
""" } @@ -44,8 +44,8 @@

Pipeline Configuration:

-

ziadbkh/bindflow

-

https://github.com/ziadbkh/bindflow

+

AustralianBioCommons/sbp-bindflow

+

https://github.com/AustralianBioCommons/sbp-bindflow

diff --git a/assets/email_template.txt b/assets/email_template.txt index beb96b2..c0cc8c4 100644 --- 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: $v" }.join("\n") %> -- -ziadbkh/bindflow -https://github.com/ziadbkh/bindflow +AustralianBioCommons/sbp-bindflow +https://github.com/AustralianBioCommons/sbp-bindflow diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 23af442..a92ab06 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,13 +1,13 @@ id: "ziadbkh-bindflow-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "ziadbkh/bindflow Methods Description" -section_href: "https://github.com/ziadbkh/bindflow" +section_name: "AustralianBioCommons/sbp-bindflow Methods Description" +section_href: "https://github.com/AustralianBioCommons/sbp-bindflow" plot_type: "html" ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using ziadbkh/bindflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

Data was processed using AustralianBioCommons/sbp-bindflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

${tool_citations}

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ee61fa2..b4cbefa 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the ziadbkh/bindflow + This report has been generated by the AustralianBioCommons/sbp-bindflow analysis pipeline. report_section_order: "ziadbkh-bindflow-methods-description": diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 1553128..6536c5e 100644 --- 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 index f976bed..4a7657d 100644 --- 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 index 38d2c0b..adc945d 100644 --- 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 diff --git a/conf/gadi_test.config b/conf/gadi_test.config index 05e0aaa..e673999 100644 --- a/conf/gadi_test.config +++ b/conf/gadi_test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run ziadbkh/bindflow -profile test, --outdir + nextflow run AustralianBioCommons/sbp-bindflow -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test.config b/conf/test.config index 0d03a52..cdd43d0 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run ziadbkh/bindflow -profile test, --outdir + nextflow run AustralianBioCommons/sbp-bindflow -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 39213d3..9a80d9e 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run ziadbkh/bindflow -profile test_full, --outdir + nextflow run AustralianBioCommons/sbp-bindflow -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/README.md b/docs/README.md index 8538655..d2352b3 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -# ziadbkh/bindflow: Documentation +# AustralianBioCommons/sbp-bindflow: Documentation -The ziadbkh/bindflow documentation is split into the following pages: +The AustralianBioCommons/sbp-bindflow documentation is split into the following pages: - [Usage](usage.md) - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. diff --git a/docs/output.md b/docs/output.md index fb1aaed..ad20e60 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# Australian-Structural-Biology-Computing/bindflow: Output +# AustralianBioCommons/sbp-bindflow: Output ## Introduction diff --git a/docs/usage.md b/docs/usage.md index 5c240fe..4522c2c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,4 +1,4 @@ -# Australian-Structural-Biology-Computing/bindflow: Usage +# AustralianBioCommons/sbp-bindflow: Usage > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ @@ -69,7 +69,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run Australian-Structural-Biology-Computing/bindflow --input ./samplesheet.csv --outdir ./results -profile docker --batches 1 --bindcraft_container ./bindcraft.img +nextflow run AustralianBioCommons/sbp-bindflow --input ./samplesheet.csv --outdir ./results -profile docker --batches 1 --bindcraft_container ./bindcraft.img ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -94,7 +94,7 @@ Do not use `-c ` to specify parameters as this will result in errors. Cust The above pipeline run specified with a params file in yaml format: ```bash -nextflow run Australian-Structural-Biology-Computing/bindflow -profile docker -params-file params.yaml +nextflow run AustralianBioCommons/sbp-bindflow -profile docker -params-file params.yaml ``` with: @@ -142,14 +142,14 @@ This will launch the pipeline with the `gadi` configuration profile. The details When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: ```bash -nextflow pull Australian-Structural-Biology-Computing/bindflow +nextflow pull AustralianBioCommons/sbp-bindflow ``` ### Reproducibility It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [Australian-Structural-Biology-Computing/bindflow releases page](https://github.com/Australian-Structural-Biology-Computing/bindflow/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [AustralianBioCommons/sbp-bindflow releases page](https://github.com/AustralianBioCommons/sbp-bindflow/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. diff --git a/main.nf b/main.nf index cd87f00..fd3bf88 100644 --- a/main.nf +++ b/main.nf @@ -1,9 +1,9 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - ziadbkh/bindflow + AustralianBioCommons/sbp-bindflow ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/ziadbkh/bindflow + Github : https://github.com/AustralianBioCommons/sbp-bindflow ---------------------------------------------------------------------------------------- */ diff --git a/modules.json b/modules.json index 96f047b..39e4951 100644 --- a/modules.json +++ b/modules.json @@ -1,6 +1,6 @@ { - "name": "ziadbkh/bindflow", - "homePage": "https://github.com/ziadbkh/bindflow", + "name": "AustralianBioCommons/sbp-bindflow", + "homePage": "https://github.com/AustralianBioCommons/sbp-bindflow", "repos": { "https://github.com/nf-core/modules.git": { "modules": { diff --git a/nextflow.config b/nextflow.config index 81f9c31..5d113e9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - ziadbkh/bindflow Nextflow config file + AustralianBioCommons/sbp-bindflow Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -159,7 +159,7 @@ profiles { // Load nf-core custom profiles from different Institutions includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Load ziadbkh/bindflow custom profiles from different institutions. +// Load AustralianBioCommons/sbp-bindflow custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bindflow.config" : "/dev/null" @@ -217,9 +217,9 @@ dag { } manifest { - name = 'ziadbkh/bindflow' + name = 'AustralianBioCommons/sbp-bindflow' author = """Ziad Al-Bkhetan""" - homePage = 'https://github.com/ziadbkh/bindflow' + homePage = 'https://github.com/AustralianBioCommons/sbp-bindflow' description = """bindcraft and others""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' diff --git a/nextflow_schema.json b/nextflow_schema.json index 1e207a1..61c0652 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/ziadbkh/bindflow/master/nextflow_schema.json", - "title": "ziadbkh/bindflow pipeline parameters", + "$id": "https://raw.githubusercontent.com/AustralianBioCommons/sbp-bindflow/master/nextflow_schema.json", + "title": "AustralianBioCommons/sbp-bindflow pipeline parameters", "description": "bindcraft and others", "type": "object", "$defs": { diff --git a/subworkflows/local/run_bindcraft.nf b/subworkflows/local/run_bindcraft.nf index 006ce71..f74ee25 100644 --- a/subworkflows/local/run_bindcraft.nf +++ b/subworkflows/local/run_bindcraft.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the ziadbkh/bindflow pipeline +// Subworkflow with functionality specific to the AustralianBioCommons/sbp-bindflow pipeline // /* diff --git a/subworkflows/local/utils_nfcore_bindflow_pipeline/main.nf b/subworkflows/local/utils_nfcore_bindflow_pipeline/main.nf index 1f4e586..cfa1525 100644 --- a/subworkflows/local/utils_nfcore_bindflow_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_bindflow_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the ziadbkh/bindflow pipeline +// Subworkflow with functionality specific to the AustralianBioCommons/sbp-bindflow pipeline // /*