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Commit 8ad14a7d authored by Venkat Malladi's avatar Venkat Malladi
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Update to include astrocyte config tests and references.

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1 merge request!27Resolve "Tests for astrocyte"
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.gitlab-ci.yml
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......@@ -6,14 +6,24 @@ before_script:
stages:
- unit
- astrocyte
- integration
user_configuration:
stage: unit
script:
- pytest -m unit
- pytest -m unit --cov=./workflow/scripts
astrocyte:
stage: astrocyte
script:
- module load astrocyte/0.3.0
- module unload nextflow
- cd ..
- astrocyte_cli validate atacseq_analysis
single_end_human:
stage: integration
only:
......
README.md
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− 5
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......@@ -25,11 +25,11 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
```
## Input files
##### 1) Fastq Files
### Fastq Files
+ You will need the full path to the files for the Bash Scipt
## Design file
### Design file
+ The Design file is a tab-delimited file with 4 columns for Single-End and 5 columns for Paired-End. Letter, numbers, and underlines can be used in the names. However, the names must begin with a letter. Columns must be as follows:
1. sample_id - The id of the sample. This will be the header in output files, please make sure it is concise
......@@ -37,7 +37,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
3. replicate - Replicate number
4. fastq_read1 - Name of fastq file 1 for SE or PE data
5. fastq_read2 - Name of fastq file 2 for PE data
+ See [HERE](/docs/design_ENCSR451NAE_PE.txt) for an example design file, paired-end
+ See [HERE](/docs/design_ENCSR265ZXX_SE.txt) for an example design file, single-end
......@@ -112,9 +112,8 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
## Citation
Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi: coming soon. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
Please cite individual programs and versions of pipeline used [HERE](docs/references.md), and the overall pipeline doi: 10.5281/zenodo.3526149. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
### Credits
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).
astrocyte_pkg.yml
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......@@ -46,12 +46,12 @@ workflow_modules:
- 'bwa/intel/0.7.12'
- 'samtools/1.4.1'
- 'sambamba/0.6.6'
- 'bedtools/2.26.0'
- 'bedtools/2.25.0'
- 'deeptools/2.5.0.1'
- 'phantompeakqualtools/1.2'
- 'macs/2.1.0-20151222'
- 'UCSC_userApps/v317'
- 'singularity/2.6.1'
- 'R/3.3.2-gccmkl'
- 'pandoc/2.7'
- 'singularity/3.0.2'
......@@ -95,7 +95,7 @@ workflow_parameters:
description: |
One or more input FASTQ files from a ATAC-seq expereiment and a design
file with the link bewetwen the same file name and sample id
regex: ".*(fastq|fq)*"
regex: ".*(fastq|fq)*gz"
- id: pairedEnd
type: select
......@@ -117,7 +117,7 @@ workflow_parameters:
- [ 'true', 'True']
- [ 'false', 'False']
description: |
The Blacklisted Regions aim to identify a comprehensive set of regions
The Blacklisted Regions aim to identify a comprehensive set of regions
that have anomalous, unstructured, high signal/read counts in next gen
sequencing experiments independent of cell line and type of experiment.
If you would like these regions excluded from replicated peaks, select
......@@ -134,12 +134,22 @@ workflow_parameters:
type: select
choices:
- [ 'GRCh38', 'Human GRCh38']
- [ 'GRCh38', 'Mouse GRCh38']
- [ 'GRCm38', 'Mouse GRCm38']
required: true
description: |
Reference species and genome used for alignment and subsequent analysis.
- id: astrocyte
type: select
choices:
- [ 'true', 'true' ]
required: true
default: 'true'
description: |
Ensure configuraton for astrocyte.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
# -----------------------------------------------------------------------------
......@@ -148,7 +158,7 @@ workflow_parameters:
# The workflow must publish all final output into $baseDir
# Name of the R module that the vizapp will run against
vizapp_r_module: 'R/3.2.1-intel'
vizapp_r_module: 'R/3.4.1-gccmkl'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
......@@ -158,8 +168,4 @@ vizapp_cran_packages:
# List of any Bioconductor packages, not provided by the modules,
# that must be made available to the vizapp
vizapp_bioc_packages:
# - qusage
# - ballgown
vizapp_github_packages:
- js229/Vennerable
vizapp_bioc_packages: []
docs/index.md
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# 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)
# BICF ATAC-seq Analysis Workflow
## Introduction
......@@ -12,22 +6,10 @@ BICF ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-
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://portal.biohpc.swmed.edu/content/). However, the pipeline should be able to run on any system that supports Nextflow.
Additionally, the pipeline is designed to work with [Astrocyte Workflow System](https://astrocyte.biohpc.swmed.edu/static/docs/index.html) using a simple web interface.
Current version of the software and issue reports are at
https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis
To download the current (working not tagged) version of the software
```bash
$ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
```
## Input files
##### 1) Fastq Files
+ You will need the full path to the files for the Bash Scipt
+ One or more input FASTQ files from a ATAC-seq experiment
## Design file
+ The Design file is a tab-delimited file with 4 columns for Single-End and 5 columns for Paired-End. Letter, numbers, and underlines can be used in the names. However, the names must begin with a letter. Columns must be as follows:
......@@ -37,7 +19,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
3. replicate - Replicate number
4. fastq_read1 - Name of fastq file 1 for SE or PE data
5. fastq_read2 - Name of fastq file 2 for PE data
+ See [HERE](/docs/design_ENCSR451NAE_PE.txt) for an example design file, paired-end
+ See [HERE](/docs/design_ENCSR265ZXX_SE.txt) for an example design file, single-end
......@@ -112,9 +94,8 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
## Citation
Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi: coming soon. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
Please cite individual programs and versions of pipeline used [HERE](docs/references.md), and the overall pipeline doi: 10.5281/zenodo.3526149. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
### Credits
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).
docs/references.md
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......@@ -40,7 +40,11 @@
13. **MultiQc**:
* 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)
14. **Nextflow**:
14. **BICF ChIP-seq Analysis Workflow**:
* Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.0). Zenodo. doi:[10.5281/zenodo.3891417](https://doi.org/10.5281/zenodo.3891417)
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.
Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.
workflow/conf/biohpc.config
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......@@ -50,7 +50,7 @@ process {
executor = 'local'
}
withName: experimentQC {
module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1', 'samtools/1.4.1', 'bedtools/2.25.0', 'singularity/2.6.1']
module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1', 'samtools/1.4.1', 'bedtools/2.25.0', 'singularity/3.0.2'']
queue = '128GB,256GB,256GBv1'
}
withName: multiqcReport {
......
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