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.
Allow additional columns in the sample sheet beyond the minimum required header. (#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)
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.
Allow additional columns in the sample sheet beyond the minimum required header. (#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)
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
champagnerun...
@@ -6,4 +6,4 @@
champagnerunpath/to/champagne/main.nf
# use a revision from github instead
champagnerunCCBR/CHAMPAGNE-rv0.1.0
-
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)
Quality control steps implemented for single-end reads¶
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.
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)
Quality control steps implemented for single-end reads¶
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.
\ No newline at end of file
diff --git a/dev/contributing/index.html b/dev/contributing/index.html
index ffa44a1..5d5044c 100644
--- a/dev/contributing/index.html
+++ b/dev/contributing/index.html
@@ -1,5 +1,5 @@
- How to contribute - CHAMPAGNE
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 7570337..237ec83 100644
--- a/dev/getting-started/index.html
+++ b/dev/getting-started/index.html
@@ -1,8 +1,8 @@
- 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.
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diff --git a/dev/index.html b/dev/index.html
index bc8a371..bf05b9d 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -1,4 +1,4 @@
- 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.
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
@@ -23,4 +23,4 @@
--inputsamplesheet.csv\--genomecustom_genome\-ccustom_genome/genome/custom_genome.config
-
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.
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.
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:
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:
# activate the conda env for development
."/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
condaactivatepy311
@@ -13,4 +13,4 @@
# add it to your PATH and PYTHONPATH with:exportPATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/bin/"exportPYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.dev/"
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/dev/sitemap.xml.gz b/dev/sitemap.xml.gz
index 53a6c56..0ebf654 100644
Binary files a/dev/sitemap.xml.gz and b/dev/sitemap.xml.gz differ
diff --git a/dev/workflow/index.html b/dev/workflow/index.html
index b4dc537..3ba9883 100644
--- a/dev/workflow/index.html
+++ b/dev/workflow/index.html
@@ -1 +1 @@
- Workflow Overview - CHAMPAGNE