docs: update from nextflow-template changes

allows changelog, contributing, etc to remain in canonical location
CCBR · Aug 31, 2023 · 0a1f1be · 0a1f1be
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diff --git a/docs/CONTRIBUTING.md → .github/CONTRIBUTING.md b/docs/CONTRIBUTING.md → .github/CONTRIBUTING.md
diff --git a/docs/CHANGELOG.md → CHANGELOG.md b/docs/CHANGELOG.md → CHANGELOG.md
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -0,0 +1,3 @@
+--8<-- "CHANGELOG.md"
+
+<!-- the contents are automatically inserted here. do not edit this file, instead edit the file specified above to make changes. -->
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -0,0 +1,3 @@
+--8<-- ".github/CONTRIBUTING.md"
+
+<!-- the contents are automatically inserted here. do not edit this file, instead edit the file specified above to make changes. -->
diff --git a/docs/contributors.md b/docs/contributors.md
@@ -0,0 +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: populate this automagically similar to https://nf-co.re/contributors? or link to GitHub contributor page? could use gh action: https://github.com/lowlighter/metrics/blob/master/source/plugins/contributors/README.md
+
+# Contributions
+
+The following members contributed to the development of the CARLISLE pipeline:
+
+- [Samantha Sevilla](https://github.com/slsevilla)
+
+SS contributed to the generating the source code and all members contributed to the main concepts and analysis.
diff --git a/docs/index.md b/docs/index.md
@@ -1,7 +1,11 @@
-TODO Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:
+<!-- the README is inserted here automatically-->
+
+--8<-- "README.md"
+
+<!--- write additional info that you only want to appear in the docs index here -->
+
+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.
diff --git a/docs/user-guide/contributions.md b/docs/user-guide/contributions.md
diff --git a/docs/user-guide/getting-started.md b/docs/user-guide/getting-started.md
@@ -1,14 +1,16 @@
+This should set the stage for all of the pipeline requirements. Examples are listed below.
+
 # Overview
 
-TODO
+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.
 
 ## 1. Getting Started
 
 ## 1.1 Introduction
 
-TODO
+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).
 
-The following are sub-commands available:
+The following are sub-commands used within CARLISLE:
 
 - initialize: initialize the pipeline
 - dryrun: predict the binding of peptides to any MHC molecule
@@ -20,13 +22,16 @@ The following are sub-commands available:
 - report: create SNAKEMAKE report
 - testrun: copies test manifests and files to WORKDIR
 
-## 1.2 Install Dependencies
+## 1.2 Setup 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.
 
-TODO
+- bedtools: "bedtools/2.30.0"
+- bedops: "bedops/2.4.40"
 
 ## 1.3 Login to the cluster
 
-TODO biowulf, frce, other cloud options?
+CARLISLE has been exclusively tested on Biowulf HPC. Login to the cluster's head node and move into the pipeline location.
 
 ```
 # ssh into cluster's head node
@@ -38,6 +43,6 @@ 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.
 
 ```
-# Start an interactive node
+# Grab an interactive node
 sinteractive --time=12:00:00 --mem=8gb  --cpus-per-task=4 --pty bash
 ```
diff --git a/docs/user-guide/output.md b/docs/user-guide/output.md
@@ -1,6 +1,8 @@
+This should include all pertitant information about output files, including extensions that differentiate files. An example is provided below.
+
 # 4. Expected Outputs
 
-TODO The following directories are created under the WORKDIR/results directory:
+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.
@@ -13,5 +15,59 @@ TODO The following directories are created under the WORKDIR/results directory:
         - rose: this directory includes the annotation output from ROSE
 
 ```
-# TODO use tree command to show working directory structure
+├── 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
 ```
diff --git a/docs/user-guide/preparing-files.md b/docs/user-guide/preparing-files.md
@@ -1,4 +1,4 @@
-TODO his should describe any input files needed, including config files, manifest files, and sample files. An example is provided below.
+This should describe any input files needed, including config files, manifest files, and sample files. An example is provided below.
 
 # 2. Preparing Files
 

diff --git a/docs/user-guide/run.md b/docs/user-guide/run.md
@@ -1,13 +1,11 @@
-TODO This should include all information about the various run commands provided within the pipeline.
+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:

diff --git a/docs/user-guide/test-info.md b/docs/user-guide/test-info.md
@@ -1,4 +1,4 @@
-TODO This should walk the user through the steps of running the pipeline using test data
+This should walk the user through the steps of running the pipeline using test data
 
 # 5. Pipeline Tutorial
 

diff --git a/docs/user-guide/troubleshooting.md b/docs/user-guide/troubleshooting.md
@@ -1,4 +1,4 @@
-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.
+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
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,15 +1,15 @@
 # Project Information
-site_name: CHAMPAGNE
+site_name: TOOL_NAME
 site_author: CCR Collaborative Bioinformatics Resource
 site_description: >-
-  CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
+  insert a one-line description of TOOL_NAME here
 # Repository
-repo_name: CCBR/CHAMPAGNE
-repo_url: https://github.com/CCBR/CHAMPAGNE
-edit_uri: https://github.com/CCBR/CHAMPAGNE/edit/main/docs/
+repo_name: CCBR/TOOL_NAME
+repo_url: https://github.com/CCBR/TOOL_NAME
+edit_uri: https://github.com/CCBR/TOOL_NAME/edit/main/docs/
 
 # Copyright
-copyright: Copyright &copy; 2023 CCBR
+copyright: Copyright &copy; 2023 CCR Collaborative Bioinformatics Resource
 
 # Configuration
 theme:
@@ -98,7 +98,8 @@ nav:
       - 3. Running the Pipeline: user-guide/run.md
       - 4. Expected Output: user-guide/output.md
       - 5. Running Test Data: user-guide/test-info.md
-  - FAQ:
       - Troubleshooting: user-guide/troubleshooting.md
-      - Contributions: user-guide/contributions.md
-  - Changelog: CHANGELOG.md
+  - FAQ:
+      - How to contribute: contributing.md
+      - Contributors: contributors.md
+  - Changelog: changelog.md