Rebrand template placeholders w/ CHAMPAGNE name

README.md

@@ -1,47 +1,12 @@
-# Nextflow Template
+# CHAMPAGNE 🍾
 
-CCBR template for creating Nextflow pipelines
+CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
 
-This template takes inspiration from nektool[^1] and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow their instructions[^2].
-
-[^1]: nektool https://github.com/beardymcjohnface/nektool
-[^2]: instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core
+ 🚧**This project is under active development. It is not yet ready for production use.** 🚧
 
 ## Getting started
 
-1. Create a new repository from this template using either of these options:
-   - [**The GitHub web interface**](https://github.com/CCBR/CCBR_NextflowTemplate):
-     Click "Use this template" and "Create a new repository", then choose an owner (CCBR) and the repository name as the new tool's name.
-   - [**The GitHub command line interface**](https://cli.github.com/):
-     ```sh
-     gh repo create CCBR/TOOL_NAME \
-        --description "One-line description of your tool" \
-        --public \
-        --template CCBR/CCBR_NextflowTemplate \
-        --confirm
-     ```
-1. Change all instances of `TOOL_NAME` throughout the repo with the actual tool name. Places include:
-   - `docs/CHANGELOG.md`
-   - `mkdocs.yml`
-   - `README.md`
-   - `pyproject.toml`
-   - `src/TOOL_NAME`
-   - `src/TOOL_NAME/CITATION`
-   - `src/TOOL_NAME/__main__.py`
-1. Edit `pyproject.toml` with correct information for your tool. You will likely need to change:
-   - author names and emails
-   - dependencies
-   - project URLs
-1. Write your nextflow workflow in `src/TOOL_NAME/workflow`.
-1. Write your documentation in `docs/` and enable GitHub Pages.
-   - In settings, go to General > Pages and select the `gh-pages` branch.
-     mkdocs will build your site under the `gh-pages` branch, and GitHub Pages will make it available at `https://ccbr.github.io/TOOL_NAME`.
-
-You can look for instances of `TOOL_NAME` in case you missed any with grep:
-
-```sh
-grep -r "TOOL_NAME" *
-```
+TODO
 
 ## Usage
 
@@ -57,7 +22,7 @@ Run the example
 TOOL_NAME run --input "Hello world"
 ```
 
-## Maintaining your tool
+## Developer notes
 
 ### Use pre-commit hooks
 
@@ -69,10 +34,18 @@ Pre-commit will run the hooks every time you commit.
 
 ### Versions
 
-Increment the version number following semantic versioning[^3] in `src/TOOL_NAME/VERSION`
+Increment the version number following semantic versioning[^3] in `src/CHAMPAGNE/VERSION`
 
 [^3]: semantic versioning guidelines https://semver.org/
 
 ### Changelog
 
 Keep the changelog up to date with any user-facing changes in `docs/CHANGELOG.md`
+
+## References
+
+This repo was originally generated from the [CCBR Nextflow Template](https://github.com/CCBR/CCBR_NextflowTemplate).
+The template takes inspiration from nektool[^1] and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow their instructions[^2].
+
+[^1]: nektool https://github.com/beardymcjohnface/nektool
+[^2]: instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core

docs/CHANGELOG.md

@@ -1,18 +1,5 @@
-## TOOL_NAME v0.1.0.apha
 
-### API-breaking changes
+## CHAMPAGNE development version
 
-- change 1
-- example 2
-
-### New features
-
-- new feat 1
-
-### Bug fixes
-
-- description of bug fixed
-
-## TOOL_NAME v0.1.0
-
-This is the first release of TOOL_NAME 🎉
+_This project is under active development_
+<!--This is the first release of CHAMPAGNE 🎉-->

docs/index.md

@@ -1,5 +1,7 @@
-Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:
+TODO Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:
 
 It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/).
 
 Also include a workflow image to summarize the pipeline.
+
+TODO: programmatically add readme contents here? similar to pkgdown.

docs/user-guide/contributions.md

@@ -1,9 +1,11 @@
-Should include a list of all contributors, including GitHub handles when appropriate. In addition, a statement of who contributed to the source code specifically, identified by initials. An example is included below.
+TODO Should include a list of all contributors, including GitHub handles when appropriate. In addition, a statement of who contributed to the source code specifically, identified by initials. An example is included below.
 
-# Contributions
+# Contributors
 
-The following members contributed to the development of the CARLISLE pipeline:
+The following members contributed to the development of CHAMPAGNE:
 
-- [Samantha Sevilla](https://github.com/slsevilla)
+- [Kelly Sovacool](https://github.com/kelly-sovacool)
+- [Vishal Koparde](https://github.com/kopardev)
 
-SS contributed to the generating the source code and all members contributed to the main concepts and analysis.
+KLS developed the source code.
+All members contributed to the main concepts and analysis.

docs/user-guide/getting-started.md

@@ -1,16 +1,15 @@
-This should set the stage for all of the pipeline requirements. Examples are listed below.
 
 # Overview
 
-The CARLISLE github repository is stored locally, and will be used for project deployment. Multiple projects can be deployed from this one point simultaneously, without concern.
+TODO
 
 ## 1. Getting Started
 
 ## 1.1 Introduction
 
-The CARLISLE Pipelie beings with raw FASTQ files and performs trimming followed by alignment using [BOWTIE2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Data is then normalized through either the use of an user-species species (IE E.Coli) spike-in control or through the determined library size. Peaks are then called using [MACS2](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html), [SEACR](https://github.com/FredHutch/SEACR), and [GoPEAKS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02707-w) with various options selected by the user. Peaks are then annotated, and summarized into reports. If designated, differential analysis is performed using [DESEQ2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html). QC reports are also generated with each project using [FASTQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [MULTIQC](https://multiqc.info/). Annotations are added using [HOMER](http://homer.ucsd.edu/homer/ngs/annotation.html) and [ROSE](https://github.com/stjude/ROSE). GSEA Enrichment analysis predictions are added using [CHIPENRICH](https://bioconductor.org/packages/devel/bioc/vignettes/chipenrich/inst/doc/chipenrich-vignette.html).
+TODO
 
-The following are sub-commands used within CARLISLE:
+The following are sub-commands available:
 
 - initialize: initialize the pipeline
 - dryrun: predict the binding of peptides to any MHC molecule
@@ -22,16 +21,13 @@ The following are sub-commands used within CARLISLE:
 - report: create SNAKEMAKE report
 - testrun: copies test manifests and files to WORKDIR
 
-## 1.2 Setup Dependencies
+## 1.2 Install Dependencies
 
-CARLISLE has several dependencies listed below. These dependencies can be installed by a sysadmin. All dependencies will be automatically loaded if running from Biowulf.
-
-- bedtools: "bedtools/2.30.0"
-- bedops: "bedops/2.4.40"
+TODO
 
 ## 1.3 Login to the cluster
 
-CARLISLE has been exclusively tested on Biowulf HPC. Login to the cluster's head node and move into the pipeline location.
+TODO biowulf, frce, other cloud options?
 
 ```
 # ssh into cluster's head node
@@ -43,6 +39,6 @@ ssh -Y [email protected]
 An interactive session should be started before performing any of the pipeline sub-commands, even if the pipeline is to be executed on the cluster.
 
 ```
-# Grab an interactive node
+# Start an interactive node
 sinteractive --time=12:00:00 --mem=8gb  --cpus-per-task=4 --pty bash
 ```

docs/user-guide/output.md

@@ -1,8 +1,7 @@
-This should include all pertitant information about output files, including extensions that differentiate files. An example is provided below.
 
 # 4. Expected Outputs
 
-The following directories are created under the WORKDIR/results directory:
+TODO The following directories are created under the WORKDIR/results directory:
 
 - alignment_stats: this directory include information on the alignment of each sample
 - peaks: this directory contains a sub-directory that relates to the quality threshold used.
@@ -15,59 +14,5 @@ The following directories are created under the WORKDIR/results directory:
         - rose: this directory includes the annotation output from ROSE
 
 ```
-├── alignment_stats
-├── bam
-├── peaks
-│   ├── 0.05
-│   │   ├── contrasts
-│   │   │   ├── contrast_id1.dedup_status
-│   │   │   └── contrast_id2.dedup_status
-│   │   ├── gopeaks
-│   │   │   ├── annotation
-│   │   │   │   ├── go_enrichment
-│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_tables
-│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_html_report
-│   │   │   │   ├── homer
-│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.gopeaks_broad.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.gopeaks_narrow.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   └── rose
-│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.12500
-│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.12500
-│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_broad.12500
-│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_narrow.12500
-│   │   │   └── peak_output
-│   │   ├── macs2
-│   │   │   ├── annotation
-│   │   │   │   ├── go_enrichment
-│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_tables
-│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_html_report
-│   │   │   │   ├── homer
-│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.motifs
-│   │   │   │   │   │   ├── homerResults
-│   │   │   │   │   │   └── knownResults
-│   │   │   │   └── rose
-│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.12500
-│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.12500
-│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.12500
-│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.12500
-│   │   │   └── peak_output
+# TODO use tree command to show working directory structure
 ```

docs/user-guide/preparing-files.md

@@ -1,4 +1,4 @@
-This should describe any input files needed, including config files, manifest files, and sample files. An example is provided below.
+TODO his should describe any input files needed, including config files, manifest files, and sample files. An example is provided below.
 
 # 2. Preparing Files
 

docs/user-guide/run.md

@@ -1,11 +1,13 @@
-This should include all information about the various run commands provided within the pipeline.
+TODO This should include all information about the various run commands provided within the pipeline.
 
 # 3. Running the Pipeline
 
 ## 3.1 Pipeline Overview
 
 The Snakemake workflow has a multiple options:
 
+TODO using quarto would allow us to generate this dynamically.
+
 ```
 Usage: bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
 1.  RUNMODE: [Type: String] Valid options:

docs/user-guide/test-info.md

@@ -1,4 +1,4 @@
-This should walk the user through the steps of running the pipeline using test data
+TODO This should walk the user through the steps of running the pipeline using test data
 
 # 5. Pipeline Tutorial
 

docs/user-guide/troubleshooting.md

@@ -1,4 +1,4 @@
-This should include basic information on how to troubleshoot the pipeline. It should also include the main pipeliner developers contact information for users to utilize, as needed.
+TODO This should include basic information on how to troubleshoot the pipeline. It should also include the main pipeliner developers contact information for users to utilize, as needed.
 
 # Troubleshooting
 

mkdocs.yml

@@ -1,12 +1,12 @@
 # Project Information
-site_name: TOOL_NAME Pipeline
-site_author: Samantha Sevilla, Ph.D.
+site_name: CHAMPAGNE
+site_author: CCR Collaborative Bioinformatics Resource
 site_description: >-
-  TOOL_NAME Pipeline
+  CHAMPAGNE
 # Repository
-repo_name: CCBR/TOOL_NAME
-repo_url: https://github.com/CCBR/TOOL_NAME
-edit_uri: https://github.com/CCBR/TOOL_NAME/edit/main/docs/
+repo_name: CCBR/CHAMPAGNE
+repo_url: https://github.com/CCBR/CHAMPAGNE
+edit_uri: https://github.com/CCBR/CHAMPAGNE/edit/main/docs/
 
 # Copyright
 copyright: Copyright © 2023 CCBR

pyproject.toml

@@ -6,12 +6,13 @@ requires = [
 build-backend = 'setuptools.build_meta'
 
 [project]
-name = 'TOOL_NAME'
+name = 'CHAMPAGNE'
 dynamic = ['version','readme']
 description = "One-line description of your tool."
 keywords = ["bioinformatics", "nextflow"]
 authors = [
-    {name = "Firstname Lastname", email = "[email protected]"},
+    {name = "Kelly Sovacool", email = "[email protected]"},
+    {name = "Vishal Koparde", email = "[email protected]"},
 ]
 maintainers = [
     {name = "CCR Collaborative Bioinformatics Resource", email = "[email protected]"},
@@ -46,16 +47,16 @@ test = [
 ]
 
 [project.scripts]
-TOOL_NAME = "TOOL_NAME.__main__:main"
+CHAMPAGNE = "CHAMPAGNE.__main__:main"
 
 [project.urls]
-Homepage = "https://ccbr.github.io/TOOL_NAME"
-Documentation = "https://ccbr.github.io/TOOL_NAME"
-Repository = "https://github.com/CCBR/TOOL_NAME"
-Changelog = "https://github.com/CCBR/TOOL_NAME/blob/main/docs/CHANGELOG.md"
+Homepage = "https://ccbr.github.io/CHAMPAGNE"
+Documentation = "https://ccbr.github.io/CHAMPAGNE"
+Repository = "https://github.com/CCBR/CHAMPAGNE"
+Changelog = "https://github.com/CCBR/CHAMPAGNE/blob/main/docs/CHANGELOG.md"
 
 [tools.setuptools]
-packages = ["TOOL_NAME"]
+packages = ["CHAMPAGNE"]
 
 [tool.setuptools.dynamic]
 version = {file = "src/VERSION"}

src/CHAMPAGNE/VERSION

@@ -0,0 +1 @@
+0.1.0

src/TOOL_NAME/__main__.py → src/CHAMPAGNE/__main__.py

@@ -70,22 +70,22 @@ def cli():
     """NextFlow-powered commandline tool to do a thing.
     \b
     For more options, run:
-    TOOL_NAME command --help"""
+    CHAMPAGNE command --help"""
     pass
 
 
 help_msg_extra = """
 \b
 CLUSTER EXECUTION:
-TOOL_NAME run ... -profile [profile],[profile],...
+CHAMPAGNE run ... -profile [profile],[profile],...
 For information on Nextflow config and profiles see:
 https://www.nextflow.io/docs/latest/config.html#config-profiles
 \b
 RUN EXAMPLES:
-Required:           TOOL_NAME run --input [file]
-Specify threads:    TOOL_NAME run ... --threads [threads]
-Enable conda:       TOOL_NAME run ... --use-conda
-Add NextFlow args:  TOOL_NAME run ... -work-dir workDir -with-docker
+Required:           CHAMPAGNE run --input [file]
+Specify threads:    CHAMPAGNE run ... --threads [threads]
+Enable conda:       CHAMPAGNE run ... --use-conda
+Add NextFlow args:  CHAMPAGNE run ... -work-dir workDir -with-docker
 """
 
 
@@ -144,7 +144,7 @@ def citation(**kwargs):
 
 cli.add_command(run)
 cli.add_command(config)
-# cli.add_command(citation) # uncomment if TOOL_NAME is published in a journal or Zenodo
+# cli.add_command(citation) # uncomment if CHAMPAGNE is published in a journal or Zenodo
 
 
 def main():