diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a54c5d7d11d173b292452f3906efd258c4b0582b..db68b44edf999757dae2d41471f6101fab4c6f36 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,11 +1,12 @@
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:
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 929e2316a228ee29b6cd6f8f23627d382b9de224..1388f66111dfc262566f7a2e4fb0c1ce745ec762 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -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
diff --git a/env.md b/env.md
deleted file mode 100644
index 54176d86aa83a2fd8cf7825ad2fee7643c6234d3..0000000000000000000000000000000000000000
--- a/env.md
+++ /dev/null
@@ -1,17 +0,0 @@
-## 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
diff --git a/workflow/main.nf b/workflow/main.nf
index 6b59b778e7502c808743977a75c457f696bcfc23..8196b54bbf6659d628a5dd125abd046e25dc851a 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -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 {