Commit c6c647d8 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update readme and add in coverage.

parent 9783455d
Pipeline #1564 failed with stages
in 55 minutes and 34 seconds
before_script:
- module add python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath
- pip install --user pytest-pythonpath pytest-cov
- module load nextflow/0.24.1-SNAPSHOT
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
......@@ -18,8 +18,9 @@ single_end_mouse:
script:
- nextflow run workflow/main.nf
- pytest -m integration
- pytest --cov=./workflow/scripts
paired_end_human:
stage: integration
script:
- nextflow run workflow/main.nf --designFile "test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'
- nextflow run workflow/main.nf --designFile "$baseDir/../test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'
# BICF ChIP-seq Pipeline
[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/build.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/)
[![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)
## 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 Dept. 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.
This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://biohpc.swmed.edu/). However, the pipeline should be able to run on any system that Nextflow supports.
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