diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 1f8eeaf..458b3ef 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,17 +1,17 @@ -# phac-nml/iridanextexample: Contributing Guidelines +# phac-nml/gasclustering: Contributing Guidelines Hi there! -Many thanks for taking an interest in improving phac-nml/iridanextexample. +Many thanks for taking an interest in improving phac-nml/gasclustering. -We try to manage the required tasks for phac-nml/iridanextexample using GitHub issues, you probably came to this page when creating one. +We try to manage the required tasks for phac-nml/gasclustering using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time. ## Contribution workflow -If you'd like to write some code for phac-nml/iridanextexample, the standard workflow is as follows: +If you'd like to write some code for phac-nml/gasclustering, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [phac-nml/iridanextexample issues](https://github.com/phac-nml/iridanextexample/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 [phac-nml/iridanextexample repository](https://github.com/phac-nml/iridanextexample) to your GitHub account +1. Check that there isn't already an issue about your idea in the [phac-nml/gasclustering issues](https://github.com/phac-nml/gasclustering/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 [phac-nml/gasclustering repository](https://github.com/phac-nml/gasclustering) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core 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 @@ -52,11 +52,11 @@ These tests are run both with the latest available version of `Nextflow` and als ## Getting help -For further information/help, please consult the [phac-nml/iridanextexample documentation](https://github.com/phac-nml/iridanextexample/). +For further information/help, please consult the [phac-nml/gasclustering documentation](https://github.com/phac-nml/gasclustering/). ## Pipeline contribution conventions -To make the phac-nml/iridanextexample 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 phac-nml/gasclustering 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 @@ -105,7 +105,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes To get started: -- Open the repo in [Codespaces](https://github.com/phac-nml/iridanextexample/codespaces) +- Open the repo in [Codespaces](https://github.com/phac-nml/gasclustering/codespaces) - Tools installed - nf-core - Nextflow diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index b104368..16f7977 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -44,4 +44,4 @@ 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 phac-nml/iridanextexample _(eg. 1.1, 1.5, 1.8.2)_ + * Version of phac-nml/gasclustering _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index f0c034e..d1d63c5 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,4 +1,4 @@ contact_links: - name: "GitHub" - url: https://github.com/phac-nml/iridanextexample + url: https://github.com/phac-nml/gasclustering about: The GitHub page for development. diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index e67ccaa..ef0f21d 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 phac-nml/iridanextexample pipeline +description: Suggest an idea for the phac-nml/gasclustering pipeline labels: enhancement body: - type: textarea diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 991988f..f7a9079 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/phac-nml/iridanextexample/tree/main/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/phac-nml/gasclustering/tree/main/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core 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 d165ffc..f7a3252 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -11,9 +11,9 @@ jobs: steps: # PRs to the phac-nml repo main branch are only ok if coming from the phac-nml repo `dev` or any `patch` branches - name: Check PRs - if: github.repository == 'phac-nml/iridanextexample' + if: github.repository == 'phac-nml/gasclustering' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/iridanextexample ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/gasclustering ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 14feafd..5abe80d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: test: name: Run pipeline with test data # Only run on push if this is the phac-nml dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/iridanextexample') }}" + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/gasclustering') }}" runs-on: ubuntu-latest strategy: matrix: diff --git a/.nf-core.yml b/.nf-core.yml index 9b916f6..e55e842 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,15 +2,15 @@ repository_type: pipeline lint: files_exist: - - assets/nf-core-iridanextexample_logo_light.png - - docs/images/nf-core-iridanextexample_logo_light.png - - docs/images/nf-core-iridanextexample_logo_dark.png + - assets/nf-core-gasclustering_logo_light.png + - docs/images/nf-core-gasclustering_logo_light.png + - docs/images/nf-core-gasclustering_logo_dark.png - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml - lib/Utils.groovy - lib/WorkflowMain.groovy - lib/NfcoreTemplate.groovy - - lib/WorkflowIridanextexample.groovy + - lib/WorkflowGasclustering.groovy files_unchanged: - assets/sendmail_template.txt - assets/email_template.html diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e6ebd4..590b1f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# phac-nml/iridanextexample: Changelog +# phac-nml/gasclustering: 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). @@ -23,7 +23,7 @@ Allowing non-gzipped FASTQ files as input. Default branch is now main. ## 1.0.0 - 2023/11/30 -Initial release of phac-nml/iridanextexample, created with the [nf-core](https://nf-co.re/) template. +Initial release of phac-nml/gasclustering, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 5c12d47..07cc911 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# phac-nml/iridanextexample: Citations +# phac-nml/gasclustering: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/README.md b/README.md index e071cd3..dac6297 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ Other parameters (defaults from nf-core) are defined in [nextflow_schema.json](n To run the pipeline, please do: ```bash -nextflow run phac-nml/iridanextexample -profile singularity -r main -latest --input assets/samplesheet.csv --outdir results +nextflow run phac-nml/gasclustering -profile singularity -r main -latest --input assets/samplesheet.csv --outdir results ``` Where the `samplesheet.csv` is structured as specified in the [Input](#input) section. @@ -90,7 +90,7 @@ There is also a pipeline execution summary output file provided (specified in th To run with the test profile, please do: ```bash -nextflow run phac-nml/iridanextexample -profile docker,test -r main -latest --outdir results +nextflow run phac-nml/gasclustering -profile docker,test -r main -latest --outdir results ``` # Legal diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json index cff2940..fee2b53 100644 --- a/assets/adaptivecard.json +++ b/assets/adaptivecard.json @@ -17,7 +17,7 @@ "size": "Large", "weight": "Bolder", "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "phac-nml/iridanextexample v${version} - ${runName}", + "text": "phac-nml/gasclustering v${version} - ${runName}", "wrap": true }, { diff --git a/assets/email_template.html b/assets/email_template.html index 3b10d4f..fa4448f 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,21 +4,21 @@ - - phac-nml/iridanextexample Pipeline Report + + phac-nml/gasclustering Pipeline Report
-

phac-nml/iridanextexample v${version}

+

phac-nml/gasclustering v${version}

Run Name: $runName

<% if (!success){ out << """
-

phac-nml/iridanextexample execution completed unsuccessfully!

+

phac-nml/gasclustering 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 @@

phac-nml/iridanextexample execution co } else { out << """
- phac-nml/iridanextexample execution completed successfully! + phac-nml/gasclustering execution completed successfully!
""" } @@ -44,8 +44,8 @@

Pipeline Configuration:

-

phac-nml/iridanextexample

-

https://github.com/phac-nml/iridanextexample

+

phac-nml/gasclustering

+

https://github.com/phac-nml/gasclustering

diff --git a/assets/email_template.txt b/assets/email_template.txt index 0c55e86..3b723ce 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -4,15 +4,15 @@ |\\ | |__ __ / ` / \\ |__) |__ } { | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, `._,._,' - phac-nml/iridanextexample v${version} + phac-nml/gasclustering v${version} ---------------------------------------------------- Run Name: $runName <% if (success){ - out << "## phac-nml/iridanextexample execution completed successfully! ##" + out << "## phac-nml/gasclustering execution completed successfully! ##" } else { out << """#################################################### -## phac-nml/iridanextexample execution completed unsuccessfully! ## +## phac-nml/gasclustering execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -35,5 +35,5 @@ Pipeline Configuration: <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> -- -phac-nml/iridanextexample -https://github.com/phac-nml/iridanextexample +phac-nml/gasclustering +https://github.com/phac-nml/gasclustering diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index a50a571..629ee0f 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,11 +1,11 @@ id: "nf-core-iridanext-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "phac-nml/iridanextexample Methods Description" -section_href: "https://github.com/phac-nml/iridanextexample" +section_name: "phac-nml/gasclustering Methods Description" +section_href: "https://github.com/phac-nml/gasclustering" plot_type: "html" data: |

Methods

-

Data was processed using phac-nml/iridanextexample 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 phac-nml/gasclustering 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 cc1689a..2a36971 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,13 +1,13 @@ report_comment: > - This report has been generated by the phac-nml/iridanextexample + This report has been generated by the phac-nml/gasclustering analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: - "phac-nml-iridanextexample-methods-description": + "phac-nml-gasclustering-methods-description": order: -1000 software_versions: order: -1001 - "phac-nml-iridanextexample-summary": + "phac-nml-gasclustering-summary": order: -1002 export_plots: true diff --git a/assets/schema_input.json b/assets/schema_input.json index b1dd3fc..137c8a1 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/schema_input.json", - "title": "phac-nml/iridanextexample pipeline - params.input schema", + "$id": "https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/schema_input.json", + "title": "phac-nml/gasclustering pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", "items": { diff --git a/assets/slackreport.json b/assets/slackreport.json index 350c725..09f8325 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "phac-nml/iridanextexample v${version} - ${runName}", + "author_name": "phac-nml/gasclustering v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/base.config b/conf/base.config index 503b044..a8639a2 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - phac-nml/iridanextexample Nextflow base config file + phac-nml/gasclustering 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/test.config b/conf/test.config index 52f31db..c291870 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 phac-nml/iridanextexample -profile test, --outdir + nextflow run phac-nml/gasclustering -profile test, --outdir ---------------------------------------------------------------------------------------- */ @@ -20,5 +20,5 @@ params { max_time = '1.h' // Input data - input = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv' + input = 'https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/samplesheet.csv' } diff --git a/conf/test_full.config b/conf/test_full.config index 319becf..592513b 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 phac-nml/iridanextexample -profile test_full, --outdir + nextflow run phac-nml/gasclustering -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ @@ -15,5 +15,5 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - input = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv' + input = 'https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/samplesheet.csv' } diff --git a/docs/README.md b/docs/README.md index db77372..5697b54 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -# phac-nml/iridanextexample: Documentation +# phac-nml/gasclustering: Documentation -The phac-nml/iridanextexample documentation is split into the following pages: +The phac-nml/gasclustering 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 69a1069..f7b9ac6 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# phac-nml/iridanextexample: Output +# phac-nml/gasclustering: Output ## Introduction diff --git a/docs/run-wes-example.json b/docs/run-wes-example.json index 7807de1..88c048e 100644 --- a/docs/run-wes-example.json +++ b/docs/run-wes-example.json @@ -13,6 +13,6 @@ "engine": "nextflow", "execute_loc": "azure" }, - "workflow_url": "https://github.com/phac-nml/iridanextexample", + "workflow_url": "https://github.com/phac-nml/gasclustering", "workflow_attachment": "" } diff --git a/docs/usage.md b/docs/usage.md index ff2ccc4..00e9978 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,4 +1,4 @@ -# phac-nml/iridanextexample: Usage +# phac-nml/gasclustering: Usage ## Introduction @@ -62,7 +62,7 @@ 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 phac-nml/iridanextexample -profile docker -params-file params.yaml +nextflow run phac-nml/gasclustering -profile docker -params-file params.yaml ``` with `params.yaml` containing: @@ -79,7 +79,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c 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 [phac-nml/iridanextexample page](https://github.com/phac-nml/iridanextexample) 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 [phac-nml/gasclustering page](https://github.com/phac-nml/gasclustering) 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. diff --git a/lib/WorkflowIridanextexample.groovy b/lib/WorkflowGasclustering.groovy similarity index 93% rename from lib/WorkflowIridanextexample.groovy rename to lib/WorkflowGasclustering.groovy index 482515f..e3ffa5d 100755 --- a/lib/WorkflowIridanextexample.groovy +++ b/lib/WorkflowGasclustering.groovy @@ -1,11 +1,11 @@ // -// This file holds several functions specific to the workflow/iridanextexample.nf in the phac-nml/iridanextexample pipeline +// This file holds several functions specific to the workflow/gasclustering.nf in the phac-nml/gasclustering pipeline // import nextflow.Nextflow import groovy.text.SimpleTemplateEngine -class WorkflowIridanextExample { +class WorkflowGasclustering { // // Check and validate parameters diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 6d0e139..e7d4c6f 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -1,5 +1,5 @@ // -// This file holds several functions specific to the main.nf workflow in the phac-nml/iridanextexample pipeline +// This file holds several functions specific to the main.nf workflow in the phac-nml/gasclustering pipeline // import nextflow.Nextflow diff --git a/main.nf b/main.nf index cd2ba58..8d8d3f1 100644 --- a/main.nf +++ b/main.nf @@ -1,9 +1,9 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - phac-nml/iridanextexample + phac-nml/gasclustering ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/phac-nml/iridanextexample + Github : https://github.com/phac-nml/gasclustering ---------------------------------------------------------------------------------------- */ @@ -39,10 +39,10 @@ WorkflowMain.initialise(workflow, params, log, args) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { IRIDANEXT } from './workflows/iridanextexample' +include { IRIDANEXT } from './workflows/gasclustering' // -// WORKFLOW: Run main phac-nml/iridanextexample analysis pipeline +// WORKFLOW: Run main phac-nml/gasclustering analysis pipeline // workflow PHACNML_IRIDANEXT { IRIDANEXT () diff --git a/modules.json b/modules.json index 3f7b665..ef9329e 100644 --- a/modules.json +++ b/modules.json @@ -1,6 +1,6 @@ { - "name": "phac-nml/iridanextexample", - "homePage": "https://github.com/phac-nml/iridanextexample", + "name": "phac-nml/gasclustering", + "homePage": "https://github.com/phac-nml/gasclustering", "repos": { "https://github.com/nf-core/modules.git": { "modules": { diff --git a/modules/local/generatesummary/main.nf b/modules/local/generatesummary/main.nf index a3d0245..ddb4020 100644 --- a/modules/local/generatesummary/main.nf +++ b/modules/local/generatesummary/main.nf @@ -17,7 +17,7 @@ process GENERATE_SUMMARY { def sorted_summaries = summaries.sort{ it[0].id } // Generate summary text: - def summary_text = "IRIDANEXTEXAMPLE Pipeline Summary\n\nSUCCESS!\n" + def summary_text = "gasclustering Pipeline Summary\n\nSUCCESS!\n" // TODO: Consider the possibility of code injection. // Should probably be moved to file processing through Python. diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 5fb6717..65b173c 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -17,7 +17,7 @@ process SAMPLESHEET_CHECK { when: task.ext.when == null || task.ext.when - script: // This script is bundled with the pipeline, in phac-nml/iridanextexample/bin/ + script: // This script is bundled with the pipeline, in phac-nml/gasclustering/bin/ """ check_samplesheet.py \\ $samplesheet \\ diff --git a/nextflow.config b/nextflow.config index bba34c0..d6ea418 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - phac-nml/iridanextexample Nextflow config file + phac-nml/gasclustering Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -195,13 +195,13 @@ dag { } manifest { - name = 'phac-nml/iridanextexample' - author = """Aaron Petkau and Eric Marinier""" - homePage = 'https://github.com/phac-nml/iridanextexample' + name = 'phac-nml/gasclustering' + author = """Aaron Petkau and Eric Marinier and Matthew Wells""" + homePage = 'https://github.com/phac-nml/gasclustering' description = """IRIDA Next Example Pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.3' + version = '1.0.0dev' doi = '' defaultBranch = 'main' } diff --git a/nextflow_schema.json b/nextflow_schema.json index f26142a..d111a3c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/phac-nml/iridanextexample/main/nextflow_schema.json", - "title": "phac-nml/iridanextexample pipeline parameters", + "$id": "https://raw.githubusercontent.com/phac-nml/gasclustering/main/nextflow_schema.json", + "title": "phac-nml/gasclustering pipeline parameters", "description": "IRIDA Next Example Pipeline", "type": "object", "definitions": { diff --git a/tests/modules/local/generatesummary/main.nf.test b/tests/modules/local/generatesummary/main.nf.test index b2eb189..b5f01ab 100644 --- a/tests/modules/local/generatesummary/main.nf.test +++ b/tests/modules/local/generatesummary/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { // check if emitted output has been created assert summary.size() == 1 - assert path(summary.get(0)).linesGzip[0].equals("IRIDANEXTEXAMPLE Pipeline Summary") + assert path(summary.get(0)).linesGzip[0].equals("gasclustering Pipeline Summary") assert path(summary.get(0)).linesGzip[4].equals("SAMPLE1:") assert path(summary.get(0)).linesGzip[5].contains("reads.1: ") assert path(summary.get(0)).linesGzip[6].contains("reads.2: ") diff --git a/workflows/iridanextexample.nf b/workflows/gasclustering.nf similarity index 98% rename from workflows/iridanextexample.nf rename to workflows/gasclustering.nf index b4b02d9..d47fa09 100644 --- a/workflows/iridanextexample.nf +++ b/workflows/gasclustering.nf @@ -13,7 +13,7 @@ def summary_params = paramsSummaryMap(workflow) // Print parameter summary log to screen log.info logo + paramsSummaryLog(workflow) + citation -WorkflowIridanextexample.initialise(params, log) +WorkflowGasclustering.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~