diff --git a/dev/404.html b/dev/404.html index fe7aecc..5d8e4bb 100644 --- a/dev/404.html +++ b/dev/404.html @@ -1 +1 @@ - CHAMPAGNE

404 - Not found

\ No newline at end of file + CHAMPAGNE

404 - Not found

\ No newline at end of file diff --git a/dev/changelog/index.html b/dev/changelog/index.html index 79908af..3bf6b5d 100644 --- a/dev/changelog/index.html +++ b/dev/changelog/index.html @@ -1,4 +1,4 @@ - Changelog - CHAMPAGNE
Skip to content

Changelog

CHAMPAGNE development version

  • Create a script (bin/champagne) to provide an interface to the champagne CLI that works out-of-the-box without the need to install the python package with pip. (#180, @kelly-sovacool)
  • However, any dependencies not in the Python Standard Library must be installed for this to work. See the dependencies list in pyproject.toml.
  • Fix configuration files for compatibility with using the GitHub repo as the source. (#173, @kelly-sovacool)
  • These equivalent commands now work:
    nextflow run CCBR/CHAMPAGNE
    + Changelog - CHAMPAGNE      

    Changelog

    CHAMPAGNE development version

    • Fix configuration files for compatibility with using the GitHub repo as the source. (#173, @kelly-sovacool)
    • These equivalent commands now work:
      nextflow run CCBR/CHAMPAGNE
       champagne run --main CCBR/CHAMPAGNE
       
    • Allow multiple samples to use the same input. (#176, @kelly-sovacool)
    • Allow additional columns in the sample sheet beyond the minimum required header. (#176, @kelly-sovacool)
    • Change the peak widths histogram type from overlay to stack. (#176, @kelly-sovacool)
    • Add a workflow entry point to download fastq files from SRA. (#176, @kelly-sovacool)
    • Add test_human profile with chipseq data from ENCODE. (#176, @kelly-sovacool)

    CHAMPAGNE 0.3.0

    New features

    • Find motifs in the genome with Homer. (#142)
    • Run motif enrichment analysis with MEME. (#142)
    • Annotate peaks with chipseeker. (#142,#147,#157)
    • Add preseq complexity curve and fastq screen to multiqc report. (#147)
    • Support multiple replicates per sample and call consensus peaks on replicates. (#129)
    • Optionally normalize p-values with the CCBR/consensus_peaks subworkflow.
    • Implement differential peak calling. (#158)
    • Optionally specify contrasts via a YAML file. If no file is specified, differential analysis is not performed.
    • If any sample has only one replicate, run MAnorm, otherwise run diffbind.
    • Print the recommended citation in bibtex format with champagne --citation. (#153)
    • CHAMPAGNE is also now archived in Zenodo with DOI 10.5281/zenodo.10516078.
    • The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)

    Bug fixes

    • Fix deepTools plots (#144):
    • Per sample fingerprint plots instead of per replicate.
    • Input normalized profile plots.
    • Protein-coding-only versions of plots.
    • Ensure sample IDs are sorted. (#150)
    • Fix a bug where the wrong SICER output file was used for downstream analyses. (#155)
    • Fix CLI profile on machines other than biowulf & FRCE. (#168)
    • Fix broken bold styling in documentation website. (#53)

    CHAMPAGNE 0.2.2

    • Fix permissions issues in the CLI. (#167)

    CHAMPAGNE 0.2.1

    • Fix a bug in QC stats that mixed up the statistics for different samples. (#125)
    • Fix a bug in the CLI that added the -profile to the nextflow command even if it wasn't needed (#125).
    • Report read counts between blacklist & filtering steps in the QC table. (#125)
    • Run spooker on workflow completion (#126).

    CHAMPAGNE 0.2.0

    New features

    • Implement peak calling with sicer2, macs2, and gem. (#52)
    • Add parameter options to skip QC, input normalization, and/or peak calling steps. (#72)
    • Calculate and plot QC metrics for called peaks:
    • Fraction in Peaks (FRiP) (#89)
    • Jaccard index (#92)
    • Histogram of peak widths (#92)
    • Add support for paired-end reads. (#105)
    • Add an option to use a custom reference from a genome fasta, gtf, and blacklist file. (#105)
    • Champagne CLI: (#112)
    • New --mode option for champagne run to execute the workflow locally ('local') or submit it as a slurm job ('slurm').
    • Option to override the path to the champagne main.nf file or specify the github repo (CCBR/CHAMPAGNE) instead.
      # use the default path
       champagne run ...
      diff --git a/dev/contributing/index.html b/dev/contributing/index.html
      index b4a049d..f51f61b 100644
      --- a/dev/contributing/index.html
      +++ b/dev/contributing/index.html
      @@ -1,4 +1,4 @@
      - How to contribute - CHAMPAGNE      

      Contributing to CHAMPAGNE

      TODO -- describe gitflow, require PRs...

      Use pre-commit hooks

      Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.

      Install pre-commit if you haven't already, then run pre-commit install to install the hooks specified in .pre-commit-config.yaml. Pre-commit will run the hooks every time you commit.

      Versions

      Increment the version number following semantic versioning1 in the VERSION file.

      Changelog

      Keep the changelog up to date with all notable changes in CHANGELOG.md2.

      VS code extensions

      If you use VS code, installing nf-core extension pack is recommended.

      Installation

      For testing and debugging, We recommend installing the dev version of champagne to a user-specific location.

      git clone https://github.com/CCBR/CHAMPAGNE
      + How to contribute - CHAMPAGNE      

      Contributing to CHAMPAGNE

      TODO -- describe gitflow, require PRs...

      Use pre-commit hooks

      Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.

      Install pre-commit if you haven't already, then run pre-commit install to install the hooks specified in .pre-commit-config.yaml. Pre-commit will run the hooks every time you commit.

      Versions

      Increment the version number following semantic versioning1 in the VERSION file.

      Changelog

      Keep the changelog up to date with all notable changes in CHANGELOG.md2.

      VS code extensions

      If you use VS code, installing nf-core extension pack is recommended.

      Installation

      For testing and debugging, We recommend installing the dev version of champagne to a user-specific location.

      git clone https://github.com/CCBR/CHAMPAGNE
       mkdir -p ~/bin/champagne
       pip install ./CHAMPAGNE -t ~/bin/champagne
       export PATH="$HOME/bin/champagne/bin:$PATH"
      diff --git a/dev/contributors/index.html b/dev/contributors/index.html
      index a612d6d..4a4ebd0 100644
      --- a/dev/contributors/index.html
      +++ b/dev/contributors/index.html
      @@ -1 +1 @@
      - Contributors - CHAMPAGNE      

      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:

      SS contributed to the generating the source code and all members contributed to the main concepts and analysis.

      \ No newline at end of file + Contributors - CHAMPAGNE

      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:

      SS contributed to the generating the source code and all members contributed to the main concepts and analysis.

      \ No newline at end of file diff --git a/dev/getting-started/index.html b/dev/getting-started/index.html index dfe88ab..9bb0140 100644 --- a/dev/getting-started/index.html +++ b/dev/getting-started/index.html @@ -1,4 +1,4 @@ - Getting Started - CHAMPAGNE

      Getting Started with CHAMPAGNE

      TODO intro paragraph

      Installation

      CHAMPAGNE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

      Prepare a sample sheet

      TODO

      Initialize

      Copy the configuration files to your current working directory

      champagne init
      + Getting Started - CHAMPAGNE      

      Getting Started with CHAMPAGNE

      TODO intro paragraph

      Installation

      CHAMPAGNE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

      Prepare a sample sheet

      TODO

      Initialize

      Copy the configuration files to your current working directory

      champagne init
       

      Run

      TODO preview, stub, mode=slurm

      TODO required params

      Run preview to view processes that will run:

      champagne run -profile test -preview
       

      Launch a stub run to view processes that will run and download containers:

      champagne run -profile test,singularity -stub
       

      Run the test dataset using the test profile:

      champagne run -profile test,singularity
      diff --git a/dev/index.html b/dev/index.html
      index 3e4738a..0afa47f 100644
      --- a/dev/index.html
      +++ b/dev/index.html
      @@ -1,4 +1,4 @@
      - CHAMPAGNE      

      CHAMPAGNE 🍾

      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

      build mkdocs DOI

      🚧 This project is under active development. It is not yet ready for production use. 🚧

      Set up

      Champagne is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

      Biowulf

      Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.

      # start an interactive node
      + CHAMPAGNE      

      CHAMPAGNE 🍾

      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

      build mkdocs DOI

      🚧 This project is under active development. It is not yet ready for production use. 🚧

      Set up

      Champagne is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

      Biowulf

      Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.

      # start an interactive node
       sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200
       # make a working directory for your project and go to it
       mkdir -p /data/$USER/chipseq
      diff --git a/dev/manifests/index.html b/dev/manifests/index.html
      new file mode 100644
      index 0000000..76dd275
      --- /dev/null
      +++ b/dev/manifests/index.html
      @@ -0,0 +1,11 @@
      + Creating Manifests - CHAMPAGNE      

      Jotting notes here

      Samplemanifest

      The following columns are required:

      • sample: sampleID; does not need to be a unique column
      • rep: replicateID of sampleID; does not need to be a unique column
      • fastq_1: absolute path to R1 of sampleID
      • fastq_2: absolute path to R1 of sampleID
      • antibody: -c sampleID for mac2; this must match a unique {sample}_{rep} format
      • control:

      Example antibody / control format for a single-end project:

      sample,rep,fastq_1,fastq_2,antibody,control
      +sample,1,/path/to/sample_1.R1.fastq.gz,,input_1,input_1
      +sample,2,/path/to/sample_2.R1.fastq.gz,,input_1,input_1
      +input,1,/path/to/sample1.R1.fastq.gz,,,
      +input,2,/path/to/sample1.R1.fastq.gz,,,
      +

      Example antibody / control format for a paired-end project:

      sample,rep,fastq_1,fastq_2,antibody,control
      +sample,1,/path/to/sample_1.R1.fastq.gz,/path/to/sample_1.R2.fastq.gz,input_1,input_1
      +sample,2,/path/to/sample_2.R1.fastq.gz,/path/to/sample_1.R2.fastq.gz,input_1,input_1
      +input,1,/path/to/input_1.R1.fastq.gz,/path/to/input_1.R2.fastq.gz,,
      +input,2,/path/to/input_2.R1.fastq.gz,/path/to/input_2.R2.fastq.gz,,
      +
      \ No newline at end of file diff --git a/dev/nextflow/index.html b/dev/nextflow/index.html index 5ac5899..55c1a50 100644 --- a/dev/nextflow/index.html +++ b/dev/nextflow/index.html @@ -1,4 +1,4 @@ - nextflow pipeline - CHAMPAGNE

      nextflow pipeline

      You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.

      nextflow run CCBR/CHAMPAGNE -profile test,singularity
      + nextflow pipeline - CHAMPAGNE      

      nextflow pipeline

      You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.

      nextflow run CCBR/CHAMPAGNE -profile test,singularity
       

      You can specify a specific version, tag, or branch on GitHub with -r:

      nextflow run CCBR/CHAMPAGNE -r v0.3.0 -profile test,singularity
       

      Create and use a custom reference genome:

      nextflow run CCBR/CHAMPAGNE -profile test -entry MAKE_REFERENCE
       nextflow run CCBR/CHAMPAGNE -profile test -c results/test/genome/custom_genome.config
      diff --git a/dev/release-guide/index.html b/dev/release-guide/index.html
      index 6c54c42..7cf4428 100644
      --- a/dev/release-guide/index.html
      +++ b/dev/release-guide/index.html
      @@ -1,4 +1,4 @@
      - Release guide - CHAMPAGNE      

      Release Guide

      How to test a pre-release on biowulf

      Install the development version of champagne.

      # activate the conda env for development
      + Release guide - CHAMPAGNE      

      Release Guide

      How to test a pre-release on biowulf

      Install the development version of champagne.

      # activate the conda env for development
       . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
       conda activate py311
       
      diff --git a/dev/search/search_index.json b/dev/search/search_index.json
      index 032cc40..07e7e5a 100644
      --- a/dev/search/search_index.json
      +++ b/dev/search/search_index.json
      @@ -1 +1 @@
      -{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Home","text":""},{"location":"#champagne","title":"CHAMPAGNE \ud83c\udf7e","text":"

      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

      \ud83d\udea7 This project is under active development. It is not yet ready for production use. \ud83d\udea7

      "},{"location":"#set-up","title":"Set up","text":"

      Champagne is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

      "},{"location":"#biowulf","title":"Biowulf","text":"

      Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.

      # start an interactive node\nsinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200\n# make a working directory for your project and go to it\nmkdir -p /data/$USER/chipseq\ncd /data/$USER/chipseq\n# load the ccbrpipeliener module\nmodule load ccbrpipeliner\n
      "},{"location":"#usage","title":"Usage","text":"

      Initialize and run champagne with test data:

      # copy the champagne config files to your current directory\nchampagne init\n# preview the champagne jobs that will run with the test dataset\nchampagne run --mode local -profile test -preview\n# launch a champagne run on slurm with the test dataset\nchampagne run --mode slurm -profile test,biowulf\n

      To run champagne on your own data, you'll need to create a sample sheet. Take a look at these examples:

      • assets/samplesheet_test.csv - mix of single and paired end reads downloaded from github.
      • assets/samplesheet_mm10.csv - single end reads on biowulf.

      Once you've created a samplesheet with paths to your fastq files, run champagne with the --input option to specify the path to your sample sheet:

      champagne run --mode slurm -profile biowulf --input samplesheet.csv --genome hg38\n

      We currently support the hg38 and mm10 genomes. If you'd like to use a custom genome, you'll need the following files:

      • genome fasta
      • genome GTF
      • blacklist fasta

      Prepare your custom reference genome with:

      champagne run --mode slurm -profile biowulf \\\n    -entry MAKE_REFERENCE \\\n    --outdir custom_genome \\\n    --genome custom_genome \\\n    --genome_fasta genome.fasta \\\n    --genes_gtf genome.gtf \\\n    --blacklist blacklist.fasta\n

      The reference files and a config file for the genome will be written in custom_genome/genome.

      Then you can run champagne using your custom genome:

      champagne run --mode slurm -profile biowulf \\\n    --input samplesheet.csv \\\n    --genome custom_genome \\\n    -c custom_genome/genome/custom_genome.config\n
      "},{"location":"#help-contributing","title":"Help & Contributing","text":"

      Come across a bug? Open an issue and include a minimal reproducible example.

      Have a question? Ask it in discussions.

      Want to contribute to this project? Check out the contributing guidelines.

      "},{"location":"#references","title":"References","text":"

      This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool1 and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions2.

      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.

      Also include a workflow image to summarize the pipeline.

      1. nektool https://github.com/beardymcjohnface/nektool \u21a9

      2. instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core \u21a9

      "},{"location":"changelog/","title":"Changelog","text":""},{"location":"changelog/#champagne-development-version","title":"CHAMPAGNE development version","text":"
      • Create a script (bin/champagne) to provide an interface to the champagne CLI that works out-of-the-box without the need to install the python package with pip. (#180, @kelly-sovacool)
      • However, any dependencies not in the Python Standard Library must be installed for this to work. See the dependencies list in pyproject.toml.
      • Fix configuration files for compatibility with using the GitHub repo as the source. (#173, @kelly-sovacool)
      • These equivalent commands now work:
        nextflow run CCBR/CHAMPAGNE\nchampagne run --main CCBR/CHAMPAGNE\n
      • Allow multiple samples to use the same input. (#176, @kelly-sovacool)
      • Allow additional columns in the sample sheet beyond the minimum required header. (#176, @kelly-sovacool)
      • Change the peak widths histogram type from overlay to stack. (#176, @kelly-sovacool)
      • Add a workflow entry point to download fastq files from SRA. (#176, @kelly-sovacool)
      • Add test_human profile with chipseq data from ENCODE. (#176, @kelly-sovacool)
      "},{"location":"changelog/#champagne-030","title":"CHAMPAGNE 0.3.0","text":""},{"location":"changelog/#new-features","title":"New features","text":"
      • Find motifs in the genome with Homer. (#142)
      • Run motif enrichment analysis with MEME. (#142)
      • Annotate peaks with chipseeker. (#142,#147,#157)
      • Add preseq complexity curve and fastq screen to multiqc report. (#147)
      • Support multiple replicates per sample and call consensus peaks on replicates. (#129)
      • Optionally normalize p-values with the CCBR/consensus_peaks subworkflow.
      • Implement differential peak calling. (#158)
      • Optionally specify contrasts via a YAML file. If no file is specified, differential analysis is not performed.
      • If any sample has only one replicate, run MAnorm, otherwise run diffbind.
      • Print the recommended citation in bibtex format with champagne --citation. (#153)
      • CHAMPAGNE is also now archived in Zenodo with DOI 10.5281/zenodo.10516078.
      • The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)
      "},{"location":"changelog/#bug-fixes","title":"Bug fixes","text":"
      • Fix deepTools plots (#144):
      • Per sample fingerprint plots instead of per replicate.
      • Input normalized profile plots.
      • Protein-coding-only versions of plots.
      • Ensure sample IDs are sorted. (#150)
      • Fix a bug where the wrong SICER output file was used for downstream analyses. (#155)
      • Fix CLI profile on machines other than biowulf & FRCE. (#168)
      • Fix broken bold styling in documentation website. (#53)
      "},{"location":"changelog/#champagne-022","title":"CHAMPAGNE 0.2.2","text":"
      • Fix permissions issues in the CLI. (#167)
      "},{"location":"changelog/#champagne-021","title":"CHAMPAGNE 0.2.1","text":"
      • Fix a bug in QC stats that mixed up the statistics for different samples. (#125)
      • Fix a bug in the CLI that added the -profile to the nextflow command even if it wasn't needed (#125).
      • Report read counts between blacklist & filtering steps in the QC table. (#125)
      • Run spooker on workflow completion (#126).
      "},{"location":"changelog/#champagne-020","title":"CHAMPAGNE 0.2.0","text":""},{"location":"changelog/#new-features_1","title":"New features","text":"
      • Implement peak calling with sicer2, macs2, and gem. (#52)
      • Add parameter options to skip QC, input normalization, and/or peak calling steps. (#72)
      • Calculate and plot QC metrics for called peaks:
      • Fraction in Peaks (FRiP) (#89)
      • Jaccard index (#92)
      • Histogram of peak widths (#92)
      • Add support for paired-end reads. (#105)
      • Add an option to use a custom reference from a genome fasta, gtf, and blacklist file. (#105)
      • Champagne CLI: (#112)
      • New --mode option for champagne run to execute the workflow locally ('local') or submit it as a slurm job ('slurm').
      • Option to override the path to the champagne main.nf file or specify the github repo (CCBR/CHAMPAGNE) instead.
        # use the default path\nchampagne run ...\n# override the path\nchampagne run path/to/champagne/main.nf\n# use a revision from github instead\nchampagne run CCBR/CHAMPAGNE -r v0.1.0\n
      "},{"location":"changelog/#bug-fixes_1","title":"Bug fixes","text":"
      • CLI:
      • Error when biowulf-specific environment variables are not defined. (#54)
      • The host is now correctly detected as biowulf via scontrol. (#75)
      • Containers:
      • Containers are now specified in process definitions instead of withName/withLabel for better control. (#69)
        • Shared containers are specified as parameters in the config file conf/containers.config.
      • No longer use --mount type=bind or --volume for making directories available to processes in containers. Instead, use Nextflow's Channel.fromPath constructor with type: 'dir'. (#71)
      "},{"location":"changelog/#api-breaking-changes","title":"API-breaking changes","text":"
      • An error is thrown when a required input file doesn't exist. (#71)
      • Previously, the workflow quietly didn't run the process(es) that required the missing file.
      • Renamed champagne config to champagne init to avoid clashing with nextflow config. (#112)
      "},{"location":"changelog/#champagne-010","title":"CHAMPAGNE 0.1.0","text":""},{"location":"changelog/#quality-control-steps-implemented-for-single-end-reads","title":"Quality control steps implemented for single-end reads","text":"
      • Trim raw reads, FastQC on raw and trimmed reads, and FastQ Screen on trimmed reads.
      • Exclude reads that align to blacklist regions, align remaining reads to the reference genome, and deduplicate.
      • Preseq on aligned reads.
      • Phantompeakqualtools on aligned and deduplicated reads.
      • Process reads with deepTools: bam coverage to generate bigwigs for each sample, summarize all bigwigs, and compute matrices relative to TSSs and scaled to metagene regions.
      • Generate plots with deepTools: PCA, profile, heatmap, spearman correlation, and fingerprint plots.
      • Summarize all quality control steps in a MultiQC report.
      • Input-normalize ChIP fragments for the next stage of the pipeline.
      "},{"location":"contributing/","title":"Contributing to CHAMPAGNE","text":"

      TODO -- describe gitflow, require PRs...

      "},{"location":"contributing/#use-pre-commit-hooks","title":"Use pre-commit hooks","text":"

      Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.

      Install pre-commit if you haven't already, then run pre-commit install to install the hooks specified in .pre-commit-config.yaml. Pre-commit will run the hooks every time you commit.

      "},{"location":"contributing/#versions","title":"Versions","text":"

      Increment the version number following semantic versioning1 in the VERSION file.

      "},{"location":"contributing/#changelog","title":"Changelog","text":"

      Keep the changelog up to date with all notable changes in CHANGELOG.md2.

      "},{"location":"contributing/#vs-code-extensions","title":"VS code extensions","text":"

      If you use VS code, installing nf-core extension pack is recommended.

      "},{"location":"contributing/#installation","title":"Installation","text":"

      For testing and debugging, We recommend installing the dev version of champagne to a user-specific location.

      git clone https://github.com/CCBR/CHAMPAGNE\nmkdir -p ~/bin/champagne\npip install ./CHAMPAGNE -t ~/bin/champagne\nexport PATH=\"$HOME/bin/champagne/bin:$PATH\"\n
      1. semantic versioning guidelines https://semver.org/ \u21a9

      2. changelog guidelines: https://keepachangelog.com/en/1.1.0/ \u21a9

      "},{"location":"contributors/","title":"Contributors","text":"

      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

      "},{"location":"contributors/#contributions","title":"Contributions","text":"

      The following members contributed to the development of the CARLISLE pipeline:

      • Samantha Sevilla

      SS contributed to the generating the source code and all members contributed to the main concepts and analysis.

      "},{"location":"getting-started/","title":"Getting Started with CHAMPAGNE","text":"

      TODO intro paragraph

      "},{"location":"getting-started/#installation","title":"Installation","text":"

      CHAMPAGNE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

      "},{"location":"getting-started/#prepare-a-sample-sheet","title":"Prepare a sample sheet","text":"

      TODO

      "},{"location":"getting-started/#initialize","title":"Initialize","text":"

      Copy the configuration files to your current working directory

      champagne init\n
      "},{"location":"getting-started/#run","title":"Run","text":"

      TODO preview, stub, mode=slurm

      TODO required params

      Run preview to view processes that will run:

      champagne run -profile test -preview\n

      Launch a stub run to view processes that will run and download containers:

      champagne run -profile test,singularity -stub\n

      Run the test dataset using the test profile:

      champagne run -profile test,singularity\n

      or explicitly specify the output directory and input:

      champagne run -profile singularity --outdir results/test --input assets/samplesheet_test.csv\n
      "},{"location":"getting-started/#custom-reference-genome","title":"Custom reference genome","text":"

      TODO different required params

      Create and use a custom reference genome:

      champagne run -profile test -entry MAKE_REFERENCE\nchampagne run -profile test -c results/test/genome/custom_genome.config\n
      "},{"location":"nextflow/","title":"nextflow pipeline","text":"

      You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.

      nextflow run CCBR/CHAMPAGNE -profile test,singularity\n

      You can specify a specific version, tag, or branch on GitHub with -r:

      nextflow run CCBR/CHAMPAGNE -r v0.3.0 -profile test,singularity\n

      Create and use a custom reference genome:

      nextflow run CCBR/CHAMPAGNE -profile test -entry MAKE_REFERENCE\nnextflow run CCBR/CHAMPAGNE -profile test -c results/test/genome/custom_genome.config\n
      "},{"location":"nextflow/#biowulf","title":"biowulf","text":"

      If you're running it on biowulf without the champagne CLI, first load the ccbrpipeliner and nextflow modules, and be sure to specify the biowulf and slurm profiles:

      module load ccbrpipeliner\nmodule load nextflow\nnextflow run CCBR/CHAMPAGNE -profile test,biowulf,slurm\n
      "},{"location":"release-guide/","title":"Release Guide","text":""},{"location":"release-guide/#how-to-test-a-pre-release-on-biowulf","title":"How to test a pre-release on biowulf","text":"

      Install the development version of champagne.

      # activate the conda env for development\n. \"/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh\"\nconda activate py311\n\n# go to the source on biowulf and update\ncd /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/champagne-dev\ngit pull\n# optionally switch to different branch if needed\n\n# install the version to a hidden path (e.g. .dev, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE\ncd ..\npip install ./champagne-dev -t ./.dev\n# add it to your PATH and PYTHONPATH with:\nexport PATH=\"$PATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/bin/\"\nexport PYTHONPATH=\"$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/\"\n
      "}]} \ No newline at end of file +{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Home","text":""},{"location":"#champagne","title":"CHAMPAGNE \ud83c\udf7e","text":"

      CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

      \ud83d\udea7 This project is under active development. It is not yet ready for production use. \ud83d\udea7

      "},{"location":"#set-up","title":"Set up","text":"

      Champagne is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

      "},{"location":"#biowulf","title":"Biowulf","text":"

      Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.

      # start an interactive node\nsinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200\n# make a working directory for your project and go to it\nmkdir -p /data/$USER/chipseq\ncd /data/$USER/chipseq\n# load the ccbrpipeliener module\nmodule load ccbrpipeliner\n
      "},{"location":"#usage","title":"Usage","text":"

      Initialize and run champagne with test data:

      # copy the champagne config files to your current directory\nchampagne init\n# preview the champagne jobs that will run with the test dataset\nchampagne run --mode local -profile test -preview\n# launch a champagne run on slurm with the test dataset\nchampagne run --mode slurm -profile test,biowulf\n

      To run champagne on your own data, you'll need to create a sample sheet. Take a look at these examples:

      • assets/samplesheet_test.csv - mix of single and paired end reads downloaded from github.
      • assets/samplesheet_mm10.csv - single end reads on biowulf.

      Once you've created a samplesheet with paths to your fastq files, run champagne with the --input option to specify the path to your sample sheet:

      champagne run --mode slurm -profile biowulf --input samplesheet.csv --genome hg38\n

      We currently support the hg38 and mm10 genomes. If you'd like to use a custom genome, you'll need the following files:

      • genome fasta
      • genome GTF
      • blacklist fasta

      Prepare your custom reference genome with:

      champagne run --mode slurm -profile biowulf \\\n    -entry MAKE_REFERENCE \\\n    --outdir custom_genome \\\n    --genome custom_genome \\\n    --genome_fasta genome.fasta \\\n    --genes_gtf genome.gtf \\\n    --blacklist blacklist.fasta\n

      The reference files and a config file for the genome will be written in custom_genome/genome.

      Then you can run champagne using your custom genome:

      champagne run --mode slurm -profile biowulf \\\n    --input samplesheet.csv \\\n    --genome custom_genome \\\n    -c custom_genome/genome/custom_genome.config\n
      "},{"location":"#help-contributing","title":"Help & Contributing","text":"

      Come across a bug? Open an issue and include a minimal reproducible example.

      Have a question? Ask it in discussions.

      Want to contribute to this project? Check out the contributing guidelines.

      "},{"location":"#references","title":"References","text":"

      This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool1 and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions2.

      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.

      Also include a workflow image to summarize the pipeline.

      1. nektool https://github.com/beardymcjohnface/nektool \u21a9

      2. instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core \u21a9

      "},{"location":"changelog/","title":"Changelog","text":""},{"location":"changelog/#champagne-development-version","title":"CHAMPAGNE development version","text":"
      • Fix configuration files for compatibility with using the GitHub repo as the source. (#173, @kelly-sovacool)
      • These equivalent commands now work:
        nextflow run CCBR/CHAMPAGNE\nchampagne run --main CCBR/CHAMPAGNE\n
      • Allow multiple samples to use the same input. (#176, @kelly-sovacool)
      • Allow additional columns in the sample sheet beyond the minimum required header. (#176, @kelly-sovacool)
      • Change the peak widths histogram type from overlay to stack. (#176, @kelly-sovacool)
      • Add a workflow entry point to download fastq files from SRA. (#176, @kelly-sovacool)
      • Add test_human profile with chipseq data from ENCODE. (#176, @kelly-sovacool)
      "},{"location":"changelog/#champagne-030","title":"CHAMPAGNE 0.3.0","text":""},{"location":"changelog/#new-features","title":"New features","text":"
      • Find motifs in the genome with Homer. (#142)
      • Run motif enrichment analysis with MEME. (#142)
      • Annotate peaks with chipseeker. (#142,#147,#157)
      • Add preseq complexity curve and fastq screen to multiqc report. (#147)
      • Support multiple replicates per sample and call consensus peaks on replicates. (#129)
      • Optionally normalize p-values with the CCBR/consensus_peaks subworkflow.
      • Implement differential peak calling. (#158)
      • Optionally specify contrasts via a YAML file. If no file is specified, differential analysis is not performed.
      • If any sample has only one replicate, run MAnorm, otherwise run diffbind.
      • Print the recommended citation in bibtex format with champagne --citation. (#153)
      • CHAMPAGNE is also now archived in Zenodo with DOI 10.5281/zenodo.10516078.
      • The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)
      "},{"location":"changelog/#bug-fixes","title":"Bug fixes","text":"
      • Fix deepTools plots (#144):
      • Per sample fingerprint plots instead of per replicate.
      • Input normalized profile plots.
      • Protein-coding-only versions of plots.
      • Ensure sample IDs are sorted. (#150)
      • Fix a bug where the wrong SICER output file was used for downstream analyses. (#155)
      • Fix CLI profile on machines other than biowulf & FRCE. (#168)
      • Fix broken bold styling in documentation website. (#53)
      "},{"location":"changelog/#champagne-022","title":"CHAMPAGNE 0.2.2","text":"
      • Fix permissions issues in the CLI. (#167)
      "},{"location":"changelog/#champagne-021","title":"CHAMPAGNE 0.2.1","text":"
      • Fix a bug in QC stats that mixed up the statistics for different samples. (#125)
      • Fix a bug in the CLI that added the -profile to the nextflow command even if it wasn't needed (#125).
      • Report read counts between blacklist & filtering steps in the QC table. (#125)
      • Run spooker on workflow completion (#126).
      "},{"location":"changelog/#champagne-020","title":"CHAMPAGNE 0.2.0","text":""},{"location":"changelog/#new-features_1","title":"New features","text":"
      • Implement peak calling with sicer2, macs2, and gem. (#52)
      • Add parameter options to skip QC, input normalization, and/or peak calling steps. (#72)
      • Calculate and plot QC metrics for called peaks:
      • Fraction in Peaks (FRiP) (#89)
      • Jaccard index (#92)
      • Histogram of peak widths (#92)
      • Add support for paired-end reads. (#105)
      • Add an option to use a custom reference from a genome fasta, gtf, and blacklist file. (#105)
      • Champagne CLI: (#112)
      • New --mode option for champagne run to execute the workflow locally ('local') or submit it as a slurm job ('slurm').
      • Option to override the path to the champagne main.nf file or specify the github repo (CCBR/CHAMPAGNE) instead.
        # use the default path\nchampagne run ...\n# override the path\nchampagne run path/to/champagne/main.nf\n# use a revision from github instead\nchampagne run CCBR/CHAMPAGNE -r v0.1.0\n
      "},{"location":"changelog/#bug-fixes_1","title":"Bug fixes","text":"
      • CLI:
      • Error when biowulf-specific environment variables are not defined. (#54)
      • The host is now correctly detected as biowulf via scontrol. (#75)
      • Containers:
      • Containers are now specified in process definitions instead of withName/withLabel for better control. (#69)
        • Shared containers are specified as parameters in the config file conf/containers.config.
      • No longer use --mount type=bind or --volume for making directories available to processes in containers. Instead, use Nextflow's Channel.fromPath constructor with type: 'dir'. (#71)
      "},{"location":"changelog/#api-breaking-changes","title":"API-breaking changes","text":"
      • An error is thrown when a required input file doesn't exist. (#71)
      • Previously, the workflow quietly didn't run the process(es) that required the missing file.
      • Renamed champagne config to champagne init to avoid clashing with nextflow config. (#112)
      "},{"location":"changelog/#champagne-010","title":"CHAMPAGNE 0.1.0","text":""},{"location":"changelog/#quality-control-steps-implemented-for-single-end-reads","title":"Quality control steps implemented for single-end reads","text":"
      • Trim raw reads, FastQC on raw and trimmed reads, and FastQ Screen on trimmed reads.
      • Exclude reads that align to blacklist regions, align remaining reads to the reference genome, and deduplicate.
      • Preseq on aligned reads.
      • Phantompeakqualtools on aligned and deduplicated reads.
      • Process reads with deepTools: bam coverage to generate bigwigs for each sample, summarize all bigwigs, and compute matrices relative to TSSs and scaled to metagene regions.
      • Generate plots with deepTools: PCA, profile, heatmap, spearman correlation, and fingerprint plots.
      • Summarize all quality control steps in a MultiQC report.
      • Input-normalize ChIP fragments for the next stage of the pipeline.
      "},{"location":"contributing/","title":"Contributing to CHAMPAGNE","text":"

      TODO -- describe gitflow, require PRs...

      "},{"location":"contributing/#use-pre-commit-hooks","title":"Use pre-commit hooks","text":"

      Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.

      Install pre-commit if you haven't already, then run pre-commit install to install the hooks specified in .pre-commit-config.yaml. Pre-commit will run the hooks every time you commit.

      "},{"location":"contributing/#versions","title":"Versions","text":"

      Increment the version number following semantic versioning1 in the VERSION file.

      "},{"location":"contributing/#changelog","title":"Changelog","text":"

      Keep the changelog up to date with all notable changes in CHANGELOG.md2.

      "},{"location":"contributing/#vs-code-extensions","title":"VS code extensions","text":"

      If you use VS code, installing nf-core extension pack is recommended.

      "},{"location":"contributing/#installation","title":"Installation","text":"

      For testing and debugging, We recommend installing the dev version of champagne to a user-specific location.

      git clone https://github.com/CCBR/CHAMPAGNE\nmkdir -p ~/bin/champagne\npip install ./CHAMPAGNE -t ~/bin/champagne\nexport PATH=\"$HOME/bin/champagne/bin:$PATH\"\n
      1. semantic versioning guidelines https://semver.org/ \u21a9

      2. changelog guidelines: https://keepachangelog.com/en/1.1.0/ \u21a9

      "},{"location":"contributors/","title":"Contributors","text":"

      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

      "},{"location":"contributors/#contributions","title":"Contributions","text":"

      The following members contributed to the development of the CARLISLE pipeline:

      • Samantha Sevilla

      SS contributed to the generating the source code and all members contributed to the main concepts and analysis.

      "},{"location":"getting-started/","title":"Getting Started with CHAMPAGNE","text":"

      TODO intro paragraph

      "},{"location":"getting-started/#installation","title":"Installation","text":"

      CHAMPAGNE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

      "},{"location":"getting-started/#prepare-a-sample-sheet","title":"Prepare a sample sheet","text":"

      TODO

      "},{"location":"getting-started/#initialize","title":"Initialize","text":"

      Copy the configuration files to your current working directory

      champagne init\n
      "},{"location":"getting-started/#run","title":"Run","text":"

      TODO preview, stub, mode=slurm

      TODO required params

      Run preview to view processes that will run:

      champagne run -profile test -preview\n

      Launch a stub run to view processes that will run and download containers:

      champagne run -profile test,singularity -stub\n

      Run the test dataset using the test profile:

      champagne run -profile test,singularity\n

      or explicitly specify the output directory and input:

      champagne run -profile singularity --outdir results/test --input assets/samplesheet_test.csv\n
      "},{"location":"getting-started/#custom-reference-genome","title":"Custom reference genome","text":"

      TODO different required params

      Create and use a custom reference genome:

      champagne run -profile test -entry MAKE_REFERENCE\nchampagne run -profile test -c results/test/genome/custom_genome.config\n
      "},{"location":"manifests/","title":"Jotting notes here","text":""},{"location":"manifests/#samplemanifest","title":"Samplemanifest","text":"

      The following columns are required:

      • sample: sampleID; does not need to be a unique column
      • rep: replicateID of sampleID; does not need to be a unique column
      • fastq_1: absolute path to R1 of sampleID
      • fastq_2: absolute path to R1 of sampleID
      • antibody: -c sampleID for mac2; this must match a unique {sample}_{rep} format
      • control:

      Example antibody / control format for a single-end project:

      sample,rep,fastq_1,fastq_2,antibody,control\nsample,1,/path/to/sample_1.R1.fastq.gz,,input_1,input_1\nsample,2,/path/to/sample_2.R1.fastq.gz,,input_1,input_1\ninput,1,/path/to/sample1.R1.fastq.gz,,,\ninput,2,/path/to/sample1.R1.fastq.gz,,,\n

      Example antibody / control format for a paired-end project:

      sample,rep,fastq_1,fastq_2,antibody,control\nsample,1,/path/to/sample_1.R1.fastq.gz,/path/to/sample_1.R2.fastq.gz,input_1,input_1\nsample,2,/path/to/sample_2.R1.fastq.gz,/path/to/sample_1.R2.fastq.gz,input_1,input_1\ninput,1,/path/to/input_1.R1.fastq.gz,/path/to/input_1.R2.fastq.gz,,\ninput,2,/path/to/input_2.R1.fastq.gz,/path/to/input_2.R2.fastq.gz,,\n
      "},{"location":"nextflow/","title":"nextflow pipeline","text":"

      You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.

      nextflow run CCBR/CHAMPAGNE -profile test,singularity\n

      You can specify a specific version, tag, or branch on GitHub with -r:

      nextflow run CCBR/CHAMPAGNE -r v0.3.0 -profile test,singularity\n

      Create and use a custom reference genome:

      nextflow run CCBR/CHAMPAGNE -profile test -entry MAKE_REFERENCE\nnextflow run CCBR/CHAMPAGNE -profile test -c results/test/genome/custom_genome.config\n
      "},{"location":"nextflow/#biowulf","title":"biowulf","text":"

      If you're running it on biowulf without the champagne CLI, first load the ccbrpipeliner and nextflow modules, and be sure to specify the biowulf and slurm profiles:

      module load ccbrpipeliner\nmodule load nextflow\nnextflow run CCBR/CHAMPAGNE -profile test,biowulf,slurm\n
      "},{"location":"release-guide/","title":"Release Guide","text":""},{"location":"release-guide/#how-to-test-a-pre-release-on-biowulf","title":"How to test a pre-release on biowulf","text":"

      Install the development version of champagne.

      # activate the conda env for development\n. \"/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh\"\nconda activate py311\n\n# go to the source on biowulf and update\ncd /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/champagne-dev\ngit pull\n# optionally switch to different branch if needed\n\n# install the version to a hidden path (e.g. .dev, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE\ncd ..\npip install ./champagne-dev -t ./.dev\n# add it to your PATH and PYTHONPATH with:\nexport PATH=\"$PATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/bin/\"\nexport PYTHONPATH=\"$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/\"\n
      "}]} \ No newline at end of file diff --git a/dev/sitemap.xml.gz b/dev/sitemap.xml.gz index 7470b3a..aa35c55 100644 Binary files a/dev/sitemap.xml.gz and b/dev/sitemap.xml.gz differ