Merge branch 'dev' into 'master'

Publish 2.0.4

See merge request !31

.gitlab-ci.yml

@@ -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

CHANGELOG.md

@@ -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

README.md

 # 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/).

docs/references.md

@@ -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.

workflow/main.nf

@@ -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