Add in astrocyte test on default singleend data.

.gitlab-ci.yml

 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:

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

env.md

-## 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

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 {