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)
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.
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.
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.
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.
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
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.
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.
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.
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/$USER/chipseq
diff --git a/dev/manifests/index.html b/dev/manifests/index.html
new file mode 100644
index 0000000..76dd275
--- /dev/null
+++ b/dev/manifests/index.html
@@ -0,0 +1,11 @@
+ Creating Manifests - CHAMPAGNE
You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.
You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.
nextflowrunCCBR/CHAMPAGNE-profiletest,singularity
You can specify a specific version, tag, or branch on GitHub with -r:
Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.
# start an interactive node\nsinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200\n# make a working directory for your project and go to it\nmkdir -p /data/$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:
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.
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)
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
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)
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":"
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.
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
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":"
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
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=\"$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/\"\n
"}]}
\ No newline at end of file
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Home","text":""},{"location":"#champagne","title":"CHAMPAGNE \ud83c\udf7e","text":"
Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.
# start an interactive node\nsinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200\n# make a working directory for your project and go to it\nmkdir -p /data/$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:
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.
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)
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
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)
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":"
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.
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
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":"
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
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