Merge branch '29-PlotProfile'

.gitlab-ci.yml

 before_script:
   - module add  python/3.6.1-2-anaconda
   - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
-  - module load  nextflow/0.31.0
+  - module load nextflow/0.31.0
   - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
 
 stages:
@@ -76,7 +76,7 @@ single_end_skip:
   only:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --astrocyte false -resume
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false -resume
   - pytest -m singleskip_true
   artifacts:
     expire_in: 2 days

astrocyte_pkg.yml

@@ -142,6 +142,15 @@ workflow_parameters:
     description: |
       Skip motif calling
 
+  - id: skipPlotProfile
+    type: select
+    required: true
+    choices:
+      - [ 'true', 'true']
+      - [ 'false', 'false']
+    description: |
+      Skip Plot Profile Analysis
+
   - id: astrocyte
     type: select
     choices:

workflow/conf/biohpc.config

@@ -44,6 +44,10 @@ process {
     module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'UCSC_userApps/v317', 'bedtools/2.26.0', 'phantompeakqualtools/1.2']
     queue = '128GB,256GB,256GBv1'
   }
+  withName: plotProfile {
+    module = ['deeptools/2.5.0.1']
+    cpus = 32
+  }
   withName: consensusPeaks {
     module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0']
     executor = 'local'
@@ -74,18 +78,21 @@ params {
       genomesize = 'hs'
       chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
       fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
+      gta = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
     }
     'GRCh37' {
       bwa = '/project/shared/bicf_workflow_ref/GRCh37'
       genomesize = 'hs'
       chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
       fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
+      gta = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
     }
     'GRCm38' {
       bwa = '/project/shared/bicf_workflow_ref/GRCm38'
       genomesize = 'mm'
       chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
       fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
+      gta = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
     }
   }
 }

workflow/main.nf

@@ -25,8 +25,10 @@ params.topPeakCount = 600
 params.astrocyte = false
 params.skipDiff = false
 params.skipMotif = false
+params.skipPlotProfile = false
 params.references = "$baseDir/../docs/references.md"
 params.multiqc =  "$baseDir/conf/multiqc_config.yaml"
+params.gtf = "/project/shared/bicf_workflow_ref/$params.genome/gencode.gtf"
 
 // Assign variables if astrocyte
 if (params.astrocyte) {
@@ -78,8 +80,10 @@ extendReadsLen = params.extendReadsLen
 topPeakCount = params.topPeakCount
 skipDiff = params.skipDiff
 skipMotif = params.skipMotif
+skipPlotProfile = params.skipPlotProfile
 references = params.references
 multiqc = params.multiqc
+gtfFile = Channel.fromPath(params.gtf)
 
 // Check design file for errors
 process checkDesignFile {
@@ -424,6 +428,7 @@ process callPeaksMACS {
   set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks
   file '*.xls' into callPeaksMACSsummit
   file('version_*.txt') into callPeaksMACSVersions
+  file("*.fc_signal.bw") into bigwigs
 
   script:
 
@@ -456,6 +461,26 @@ peaksDesign = experimentPeaks
               "$sampleId\t$peak\t$fcSignal\t$pvalueSignal\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
               .collectFile(name:'design_peak.tsv', seed:"sample_id\tpeaks\tfc_signal\tpvalue_signal\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
 
+//plotProfile
+process plotProfile {
+  publishDir "$outDir/${task.process}", mode: 'copy'
+
+  input:
+
+  file ("*.pooled.fc_signal.bw") from bigwigs.collect()
+  file gtf from gtfFile
+
+  when:
+
+  !skipPlotProfile
+
+  script:
+  """
+  module load deeptools/2.5.0.1
+  bash $baseDir/scripts/plotProfile.sh
+  """
+}
+
 // Calculate Consensus Peaks
 process consensusPeaks {
 
@@ -575,7 +600,6 @@ process diffPeaks {
 
 // Generate Multiqc Report, gerernate Software Versions and references
 process multiqcReport {
-
   publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
@@ -611,6 +635,7 @@ process multiqcReport {
   module load multiqc/1.7
   echo $workflow.nextflow.version > version_nextflow.txt
   multiqc --version > version_multiqc.txt
+  python --version &> version_python.txt
   python3 $baseDir/scripts/generate_references.py -r $references -o software_references
   python3 $baseDir/scripts/generate_versions.py -o software_versions
   multiqc -c $multiqc .

workflow/nextflow.config

@@ -7,8 +7,8 @@ profiles {
 manifest {
   name = 'chipseq_analysis'
   description = 'BICF ChIP-seq Analysis Workflow.'
-  homePage = 'https://github.com/nf-core/rnaseq'
-  version = '1.0.0'
+  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis'
+  version = '1.0.6'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.31.0'
 }

workflow/scripts/generate_versions.py

@@ -46,6 +46,7 @@ SOFTWARE_REGEX = {
     'MEME-ChIP': ['motifSearch_vf/version_memechip.txt', r"Version (\S+)"],
     'DiffBind': ['diffPeaks_vf/version_DiffBind.txt', r"Version (\S+)\""],
     'deepTools': ['experimentQC_vf/version_deeptools.txt', r"deeptools (\S+)"],
+    'Python': ['version_python.txt', r"python, version (\S+)"],
     'MultiQC': ['version_multiqc.txt', r"multiqc, version (\S+)"],
 }
 
@@ -108,6 +109,7 @@ def main():
     results['DiffBind'] = '<span style="color:#999999;\">Not Run</span>'
     results['deepTools'] = '<span style="color:#999999;\">Not Run</span>'
     results['MultiQC'] = '<span style="color:#999999;\">Not Run</span>'
+    results['Python'] = '<span style="color:#999999;\">Not Run</span>'
 
     # list all files
     files = glob.glob('**/*.txt', recursive=True)

workflow/scripts/plotProfile.sh

+#!/bin/bash
+#plotProfile.sh
+
+bws=`ls *.bw`
+gtf=`ls *.gtf *.bed`
+
+computeMatrix reference-point \
+	--referencePoint TSS \
+	-S $bws \
+	-R $gtf \
+	--skipZeros \
+	-o computeMatrix.gz
+
+plotProfile -m computeMatrix.gz \
+	-out plotProfile.png \