Commit 64368529 authored by Venkat Malladi's avatar Venkat Malladi

Merge branch 'dev' into 'master'

Publish 2.0.4

See merge request !31
parents 1d36bc4d 66c9f064
Pipeline #7754 passed with stages
in 40 seconds
......@@ -18,7 +18,7 @@ user_configuration:
astrocyte:
stage: astrocyte
script:
- module load astrocyte/0.2.0
- module load astrocyte/0.3.1
- module unload nextflow
- cd ..
- astrocyte_cli validate atacseq_analysis
......
......@@ -2,6 +2,11 @@
All notable changes to this project will be documented in this file.
## [publish_2.0.4 ] - 2020-07-31
### Upgraded
- Updated support for astrocyte 0.3.1
- Added queue information to fix memory issue
## [publish_2.0.3 ] - 2020-06-21
### Fixed
- Removed biosample, factor, treatment from design file
......
# Astrocyte ATAC-seq analysis Workflow Package
[![pipeline Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)
[![Coverage Report](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
)](https://www.nextflow.io/)
[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.1.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
|*master*|*dev*|
|:-:|:-:|
|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/dev/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/dev)|
|[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)|[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/dev/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/dev)|
[![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%A50.3.1-blue)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3526148.svg)](https://doi.org/10.5281/zenodo.3526148)
## Introduction
BICF ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data analysis at [BICF](http://www.utsouthwestern.edu/labs/bioinformatics/) at [UT Southwestern Department of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
......
......@@ -42,7 +42,7 @@
14. **BICF ChIP-seq Analysis Workflow**:
* Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.1). Zenodo. doi:[10.5281/zenodo.3891417](https://doi.org/10.5281/zenodo.3891417)
* Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.4). Zenodo. doi:[10.5281/zenodo.3968525](https://doi.org/10.5281/zenodo.3968525)
15. **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.
......
......@@ -213,6 +213,7 @@ process alignReads {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}/${sampleId}", mode: 'copy'
queue '256GB,256GBv1'
input:
set sampleId, reads, experimentId, replicate, fqLength from trimmedReads
......@@ -264,6 +265,7 @@ process filterReads {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}/${sampleId}", mode: 'copy'
queue '128GB,256GB,256GBv1'
input:
set sampleId, mapped, experimentId, replicate from mappedReads
......@@ -326,6 +328,7 @@ process convertReads {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}", mode: 'copy'
queue '128GB,256GB,256GBv1'
input:
set sampleId, deduped, bai, experimentId, replicate from convertReads
......@@ -501,6 +504,7 @@ process callPeaksMACS {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}/${experimentId}/${replicate}", mode: 'copy'
queue '128GB,256GB,256GBv1'
input:
set sampleId, tagAlign, xcor, experimentId, replicate from experimentRows
......@@ -638,6 +642,7 @@ process peakAnnotation {
process experimentQC {
publishDir "${outDir}/${task.process}", mode: 'copy'
queue '128GB,256GB,256GBv1'
input:
file designExperimentQC
......
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