Commit 3247bebb authored by Venkat Malladi's avatar Venkat Malladi

Getting Ready for release 1.1.0

parent cd538cbf
Pipeline #6614 canceled with stages
in 2 minutes and 11 seconds
......@@ -78,9 +78,15 @@ paired_end_diff:
- master
stage: multiple
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -with-dag flowchart.pdf
- pytest -m pairedend
- pytest -m paireddiff
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- flowchart.pdf
expire_in: 7 days
single_end_skip:
stage: skip
......@@ -90,7 +96,6 @@ single_end_skip:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false
- pytest -m singleskip_true
cleanup_job:
stage: cleanup
script:
......
......@@ -6,6 +6,7 @@ These are the most common things requested on pull requests (PRs).
- [ ] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [ ] Replace dag.png with the most recent CI pipleine integrated_pe artifact
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
......@@ -2,19 +2,22 @@
All notable changes to this project will be documented in this file.
## [Unreleased]
- Fix references.md link in citation of README.md
## [publish_1.0.6 ] - 2020-04-21
### Added
- Add Nextflow to references.md
- Fix pool_and_psuedoreplicate.py to run single experiment
- Add test data for test_pool_and_pseudoreplicate
- Add PlotProfile Option
- Add Python version to MultiQC
- Add and Update tests
- Use GTF files instead of TxDb and org libraries in Annotate Peaks
- Make gtf and geneName files as param inputs
- Add test data for single control and single replicate
### Fixed
- Fix references.md link in citation of README.md
- Fix pool_and_psuedoreplicate.py to run single experiment
- Fix xcor to increase file size for --random-source
- Fix skip diff test for paired-end data
- Add test data for single control and single replicate
- Fix python version for MultiQC report
- Fix xcor to get lowest non zero value above 50
- Fix references to display in Multiqc report
......
# **CHIPseq Manual**
## Version 1.0.6
## May 31, 2019
# **ChIP-seq Manual**
## Version 1.1,0
## April 21, 2020
# BICF ChIP-seq Pipeline
|*master*|*dev*|
|:-:|:-:|
|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/dev/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/dev)|
|[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)|[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/dev/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/dev)|
[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.31.0-brightgreen)](https://www.nextflow.io/)
[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.2.0-blue)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2648845.svg)](https://doi.org/10.5281/zenodo.2648845)
## Introduction
BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at [BICF](http://www.utsouthwestern.edu/labs/bioinformatics/) at [UT Southwestern Department of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
BICF ChIP-seq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at [BICF](http://www.utsouthwestern.edu/labs/bioinformatics/) at [UT Southwestern Department of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
......@@ -60,7 +60,10 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
- --designFile '/path/to/file/design.txt',
- --genome 'GRCm38', 'GRCh38', or 'GRCh37' (if you need to use another genome contact the [BICF](mailto:BICF@UTSouthwestern.edu))
- --pairedEnd 'true' or 'false' (where 'true' is PE and 'false' is SE; default 'false')
- --outDir (optional) path and folder name of the output data, example: /home2/s000000/Desktop/Chipseq_output (if not specficied will be under workflow/output/)
- --skipDiff 'true' or 'false' (where 'true' is skip differential peak and 'false' is do peak differential peak calling; default 'false')
- --skipMotif 'true' or 'false' (where 'true' is skip motif calling and 'false' is do motif calling; default 'false')
- --skipPlotProfile 'true' or 'false' (where 'true' is skip metageneplot for TSS and 'false' is do metageneplot for TSS; default 'false')
- --outDir (optional) path and folder name of the output data, example: /home2/s000000/Desktop/Chipseq_output (if not specified will be under workflow/output/)
## Pipeline
+ There are 11 steps to the pipeline
......
......@@ -9,7 +9,7 @@
# A unique identifier for the workflow package, text/underscores only
name: 'chipseq_analysis_bicf'
# Who wrote this?
author: 'Holly Ruess, Spencer D. Barnes, Beibei Chen and Venkat Malladi'
author: 'Holly Ruess, Spencer D. Barnes, Jeremy A. Mathews, Beibei Chen and Venkat Malladi'
# A contact email address for questions
email: 'bicf@utsouthwestern.edu'
# A more informative title for the workflow package
......@@ -52,6 +52,7 @@ workflow_modules:
- 'R/3.3.2-gccmkl'
- 'meme/4.11.1-gcc-openmpi'
- 'pandoc/2.7'
- 'singularity/3.0.2'
# A list of parameters used by the workflow, defining how to present them,
......
No preview for this file type
......@@ -52,7 +52,7 @@
* Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
17. **BICF ChIP-seq Analysis Workflow**:
* Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, and Venkat S. Malladi. 2019. BICF ChIP-seq Analysis Workflow (publish_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
* Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, and Venkat S. Malladi. 2020. BICF ChIP-seq Analysis Workflow (publish_1.1.0). Zenodo. doi:[10.5281/zenodo.3759481](https://doi.org/10.5281/zenodo.3759481)
18. **Nextflow**:
* Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.
......
......@@ -4,11 +4,28 @@ profiles {
}
}
trace {
enabled = true
file = 'pipeline_trace.txt'
fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
}
timeline {
enabled = true
file = 'timeline.html'
}
report {
enabled = true
file = 'report.html'
}
manifest {
name = 'chipseq_analysis'
description = 'BICF ChIP-seq Analysis Workflow.'
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis'
version = '1.0.6'
version = '1.1.0'
mainScript = 'main.nf'
nextflowVersion = '>=0.31.0'
}
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