Commit c37ec8eb authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add in astrocyte test on default singleend data.

parent b47a158e
Pipeline #2821 failed with stages
in 23 seconds
before_script:
- module add python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath pytest-cov
- module load nextflow/0.31.0
- module load nextflow/0.31.0
- ln -s /work/BICF/s163035/chipseq/*fastq.gz test_data/
stages:
- unit
- astrocyte
- single
- multiple
......@@ -15,6 +16,18 @@ user_configuration:
- pytest -m unit
- pytest -m unit --cov=./workflow/scripts
astrocyte:
stage: astrocyte
script:
- module load astrocyte/0.1.0
- module unload nextflow
- cd ..
- astrocyte_cli validate chipseq_analysis
- astrocyte_cli test chipseq_analysis
- pytest -m singleend
artifacts:
expire_in: 2 days
single_end_mouse:
stage: single
script:
......
......@@ -11,7 +11,7 @@ name: 'chipseq_analysis_bicf'
# Who wrote this?
author: 'Beibei Chen and Venkat Malladi'
# A contact email address for questions
email: 'biohpc-help@utsouthwestern.edu'
email: 'bicf@utsouthwestern.edu'
# A more informative title for the workflow package
title: 'BICF ChIP-seq Analysis Workflow'
# A summary of the workflow package in plain text
......@@ -27,7 +27,7 @@ description: |
# web interface. These files are in the 'docs' subdirectory. The first file
# listed will be used as a documentation index and is index.md by convention
documentation_files:
- ['index.md', 'chipseq-analysis']
- 'index.md'
# -----------------------------------------------------------------------------
# NEXTFLOW WORKFLOW CONFIGURATION
......@@ -42,15 +42,16 @@ workflow_modules:
- 'python/3.6.1-2-anaconda'
- 'trimgalore/0.4.1'
- 'bwa/intel/0.7.12'
- 'samtools/1.6'
- 'sambamba/0.6.6'
- 'bedtools/2.26.0'
- 'deeptools/2.5.0.1'
- 'phantompeakqualtools/1.2'
- 'macs/2.1.0-20151222'
- 'UCSC_userApps/v317'
- 'R/3.4.1-gccmkl'
- 'R/3.3.2-gccmkl'
- 'meme/4.11.1-gcc-openmpi'
- 'python/2.7.x-anaconda'
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
......@@ -93,6 +94,7 @@ workflow_parameters:
One or more input FASTQ files from a ChIP-seq expereiment and a design
file with the link bewetwen the same file name and sample id
regex: ".*(fastq|fq)*"
min: 2
- id: pairedEnd
type: select
......@@ -117,14 +119,23 @@ workflow_parameters:
- id: genome
type: select
required: true
choices:
- [ 'GRCh38', 'Human GRCh38']
- [ 'GRCh37', 'Human GRCh37']
- [ 'GRCm38', 'Mouse GRCm38']
required: true
description: |
Reference species and genome used for alignment and subsequent analysis.
- id: astrocyte
type: select
required: true
choices:
- [ 'true', 'True']
default: 'true'
description: |
Ensure configuraton for astrocyte
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
......@@ -145,7 +156,6 @@ 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
## Create new env in specific folder
```shell
conda create -p /project/shared/bicf_workflow_ref/chipseq_bchen4/ -c r r-essentials
#Add channels
conda config --add channels conda-forge
conda config --add channels r
conda config --add channels bioconda
pip install --user twobitreader
conda install -c r r-xml
```
Install bioconductor in R console:
```R
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("DiffBind","ChIPseeker"))
```
\ No newline at end of file
......@@ -5,19 +5,33 @@
// Define Input variables
params.reads = "$baseDir/../test_data/*.fastq.gz"
params.pairedEnd = false
params.pairedEnd = 'false'
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
params.genome = 'GRCm38'
params.genomes = []
params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
params.topPeakCount = 600
// Assign variables if astrocyte
params.genome = 'GRCm38'
if (params.astrocyte == 'false') {
params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
} else if (params.astrocyte == 'true') {
referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$genome"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.chromSizes = 'hs'
} else if (params.chromSizes == 'GRCm38') {
params.chromSizes = 'mm'
}
}
// Check inputs
if( params.bwaIndex ){
bwaIndex = Channel
......@@ -35,7 +49,6 @@ readsList = Channel
.collectFile( name: 'fileList.tsv', newLine: true )
// Define regular variables
pairedEnd = params.pairedEnd
designFile = params.designFile
genomeSize = params.genomeSize
genome = params.genome
......@@ -46,6 +59,12 @@ outDir = params.outDir
extendReadsLen = params.extendReadsLen
topPeakCount = params.topPeakCount
if (params.pairedEnd == 'false'){
pairedEnd = false
} else {
pairedEnd = true
}
// Check design file for errors
process checkDesignFile {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment