Getting Ready for release 1.1.0

.gitlab-ci.yml

@@ -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:

.gitlab/merge_request_templates/merge_request.md

@@ -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

CHANGELOG.md

@@ -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

README.md

-# **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

astrocyte_pkg.yml

@@ -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,

docs/references.md

@@ -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.

workflow/nextflow.config

@@ -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'
 }