diff --git a/docs/CONTRIBUTING.md b/.github/CONTRIBUTING.md similarity index 100% rename from docs/CONTRIBUTING.md rename to .github/CONTRIBUTING.md diff --git a/docs/CHANGELOG.md b/CHANGELOG.md similarity index 100% rename from docs/CHANGELOG.md rename to CHANGELOG.md diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 00000000..bebc5793 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,3 @@ +--8<-- "CHANGELOG.md" + + diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 00000000..773a7e50 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,3 @@ +--8<-- ".github/CONTRIBUTING.md" + + diff --git a/docs/contributors.md b/docs/contributors.md new file mode 100644 index 00000000..a5d1b853 --- /dev/null +++ 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 index 23741c46..b4655edf 100644 --- 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: + + +--8<-- "README.md" + + + +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 deleted file mode 100644 index 5a0c6495..00000000 --- a/docs/user-guide/contributions.md +++ /dev/null @@ -1,11 +0,0 @@ -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. - -# Contributors - -The following members contributed to the development of CHAMPAGNE: - -- [Kelly Sovacool](https://github.com/kelly-sovacool) -- [Vishal Koparde](https://github.com/kopardev) - -KLS developed the source code. -All members contributed to the main concepts and analysis. diff --git a/docs/user-guide/getting-started.md b/docs/user-guide/getting-started.md index 67b0ed0e..fbb07443 100644 --- 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 $USER@biowulf.nih.gov 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 index 03b8bb6b..dd5bee57 100644 --- 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 index 56aa5b6e..5ba6f0d4 100644 --- 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 index 9b3d3f54..493caab9 100644 --- a/docs/user-guide/run.md +++ b/docs/user-guide/run.md @@ -1,4 +1,4 @@ -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 @@ -6,8 +6,6 @@ TODO This should include all information about the various run commands provided 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= -w/--workdir= 1. RUNMODE: [Type: String] Valid options: diff --git a/docs/user-guide/test-info.md b/docs/user-guide/test-info.md index 8e606d0c..ac02374b 100644 --- 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 index 27b3bdaa..3ac52343 100644 --- 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 index 364ede15..f61def2f 100644 --- 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 © 2023 CCBR +copyright: Copyright © 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