test_data/design_single_contol_SE.txt

+sample_id	experiment_id	biosample	factor	treatment	replicate	control_id	fastq_read1
+ENCLB497XZB	ENCSR000DXB	Panc1	H3K4me3	None	1	ENCLB304SBJ	ENCFF001GBW.fastq.gz
+ENCLB304SBJ	ENCSR000DXC	Panc1	Control	None	1	ENCLB304SBJ	ENCFF001HWJ.fastq.gz

test_data/fetch_test_data.sh

@@ -25,3 +25,9 @@ wget https://www.encodeproject.org/files/ENCFF161HBP/@@download/ENCFF161HBP.fast
 wget https://www.encodeproject.org/files/ENCFF776KZU/@@download/ENCFF776KZU.fastq.gz
 wget https://www.encodeproject.org/files/ENCFF119KHM/@@download/ENCFF119KHM.fastq.gz
 echo "Done with Paired-end"
+
+echo "Downloading Single-end data set Human ENCSR000DXB and ENCSR000DXC"
+wget https://www.encodeproject.org/files/ENCFF001GBW/@@download/ENCFF001GBW.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001GBV/@@download/ENCFF001GBV.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001HWJ/@@download/ENCFF001HWJ.fastq.gz
+echo "Done with Single-end"

test_data/test_cross.qc

+Test.20.tagAlign.gz	18588987	0,20,33	0.211525291335199,0.211232019956852,0.211139666755398	35	0.2123067	1500	0.209429	1.01001	0.7284536       0

workflow/conf/biohpc.config

@@ -2,6 +2,7 @@ process {
   executor = 'slurm'
   queue = 'super'
   clusterOptions = '--hold'
+  beforeScript= 'ulimit -Ss unlimited'
 
   // Process specific configuration
   withName: checkDesignFile {
@@ -44,6 +45,10 @@ 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'
@@ -61,7 +66,7 @@ process {
     cpus = 32
   }
   withName: multiqcReport {
-    module = ['python/3.6.1-2-anaconda', 'pandoc/2.7', 'multiqc/1.7']
+    module = ['python/3.6.1-2-anaconda', 'pandoc/2.7', 'singularity/3.0.2']
     executor = 'local'
   }
 }
@@ -70,22 +75,28 @@ params {
   // Reference file paths on BioHPC
   genomes {
     'GRCh38' {
-      bwa = '/project/shared/bicf_workflow_ref/GRCh38'
+      bwa = '/project/shared/bicf_workflow_ref/human/GRCh38'
       genomesize = 'hs'
-      chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
-      fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
+      chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh38/genomefile.txt'
+      fasta = '/project/shared/bicf_workflow_ref/human/GRCh38/genome.fa'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh38/gencode.v25.chr_patch_hapl_scaff.annotation.gtf'
+      geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
     }
     'GRCh37' {
-      bwa = '/project/shared/bicf_workflow_ref/GRCh37'
+      bwa = '/project/shared/bicf_workflow_ref/human/GRCh37'
       genomesize = 'hs'
-      chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
-      fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
+      chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh37/genomefile.txt'
+      fasta = '/project/shared/bicf_workflow_ref/human/GRCh37/genome.fa'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh37/gencode.v19.chr_patch_hapl_scaff.annotation.gtf'
+      geneNames = '/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt'
     }
     'GRCm38' {
-      bwa = '/project/shared/bicf_workflow_ref/GRCm38'
+      bwa = '/project/shared/bicf_workflow_ref/mouse/GRCm38'
       genomesize = 'mm'
-      chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
-      fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
+      chromsizes = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genomefile.txt'
+      fasta = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genome.fa'
+      gtf = '/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf'
+      geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
     }
   }
 }

workflow/conf/multiqc_config.yaml

+# Custom Logo
+custom_logo: 'bicf_logo.png'
+custom_logo_url: 'https://www.utsouthwestern.edu/labs/bioinformatics/'
+custom_logo_title: 'Bioinformatics Core Facility'
+
+report_header_info:
+    - Contact E-mail: 'bicf@utsouthwestern.edu'
+    - Application Type: 'ChIP-seq'
+    - Department: 'Bioinformatic Core Facility, Department of Bioinformatics'
+    - Contributors and Licensing: 'See https://doi.org/10.5281/zenodo.2648844'
+
+
 # Title to use for the report.
 title: BICF ChIP-seq Analysis Report
 

workflow/main.nf

 #!/usr/bin/env nextflow
 
+/*
+
+BICF ChIP-seq Analysis Workflow
+#### Homepage / Documentation
+https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/
+Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+
+
+*/
+
 // Path to an input file, or a pattern for multiple inputs
 // Note - $baseDir is the location of this workflow file main.nf
 
 // 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.cutoffRatio = 1.2
 params.outDir= "$baseDir/output"
 params.extendReadsLen = 100
 params.topPeakCount = 600
-params.astrocyte = 'false'
+params.astrocyte = false
 params.skipDiff = false
 params.skipMotif = false
+params.skipPlotProfile = false
 params.references = "$baseDir/../docs/references.md"
 params.multiqc =  "$baseDir/conf/multiqc_config.yaml"
+params.ci = false
+params.dev = false
+
 
 // Assign variables if astrocyte
 if (params.astrocyte) {
   print("Running under astrocyte")
   referenceLocation = "/project/shared/bicf_workflow_ref"
-  params.bwaIndex = "$referenceLocation/$params.genome"
-  params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
-  params.fasta = "$referenceLocation/$params.genome/genome.fa.txt"
-  if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
+  if (params.genome == 'GRCh37') {
+    params.bwaIndex = "$referenceLocation/human/$params.genome"
+    params.chromSizes = "$referenceLocation/human/$params.genome/genomefile.txt"
+    params.fasta = "$referenceLocation/human/$params.genome/genome.fa"
+    params.gtf = "$referenceLocation/human/$params.genome/gencode.v19.chr_patch_hapl_scaff.annotation.gtf"
+    params.geneNames = "$referenceLocation/human/$params.genome/genenames.txt"
     params.genomeSize = 'hs'
   } else if (params.genome == 'GRCm38') {
+    params.bwaIndex = "$referenceLocation/mouse/$params.genome"
+    params.chromSizes = "$referenceLocation/mouse/$params.genome/genomefile.txt"
+    params.fasta = "$referenceLocation/mouse/$params.genome/genome.fa"
+    params.gtf = "$referenceLocation/mouse/$params.genome/gencode.vM20.annotation.gtf"
+    params.geneNames = "$referenceLocation/mouse/$params.genome/genenames.txt"
     params.genomeSize = 'mm'
+  } else if (params.genome == 'GRCh38') {
+    params.bwaIndex = "$referenceLocation/human/$params.genome"
+    params.chromSizes = "$referenceLocation/human/$params.genome/genomefile.txt"
+    params.fasta = "$referenceLocation/human/$params.genome/genome.fa"
+    params.gtf = "$referenceLocation/human/$params.genome/gencode.v25.chr_patch_hapl_scaff.annotation.gtf"
+    params.geneNames = "$referenceLocation/human/$params.genome/genenames.txt"
+    params.genomeSize = 'hs'
   }
 } else {
     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.gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false
+    params.geneNames = params.genome ? params.genomes[ params.genome ].geneNames ?: false : false
 }
 
 
@@ -56,7 +86,8 @@ readsList = Channel
   .collectFile( name: 'fileList.tsv', newLine: true )
 
 // Define regular variables
-designFile = params.designFile
+pairedEnd = params.pairedEnd
+designFile = Channel.fromPath(params.designFile)
 genomeSize = params.genomeSize
 genome = params.genome
 chromSizes = params.chromSizes
@@ -67,15 +98,37 @@ extendReadsLen = params.extendReadsLen
 topPeakCount = params.topPeakCount
 skipDiff = params.skipDiff
 skipMotif = params.skipMotif
+skipPlotProfile = params.skipPlotProfile
 references = params.references
 multiqc = params.multiqc
+gtfFile = params.gtf
+geneNames = params.geneNames
 
-if (params.pairedEnd == 'false'){
-  pairedEnd = false
-} else {
-  pairedEnd = true
+/*
+ * trackStart: track start of pipeline
+ */
+
+process trackStart {
+  script:
+  """
+  hostname
+  ulimit -a
+
+  curl -H 'Content-Type: application/json' -X PUT -d '{ \
+      "sessionId": "${workflow.sessionId}", \
+      "pipeline": "chipseq_analysis", \
+      "start": "${workflow.start}", \
+      "astrocyte": ${params.astrocyte}, \
+      "status": "started", \
+      "nextflowVersion": "${workflow.nextflow.version}", \
+      "pipelineVersion": "1.1.2", \
+      "ci": ${params.ci}, \
+      "dev": ${params.dev}}' \
+  "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
+  """
 }
 
+
 // Check design file for errors
 process checkDesignFile {
 
@@ -83,7 +136,7 @@ process checkDesignFile {
 
   input:
 
-  designFile
+  file designFile
   file readsList
 
   output:
@@ -331,6 +384,8 @@ process crossReads {
   }
   else {
     """
+    module load python/3.6.1-2-anaconda
+    module load phantompeakqualtools/1.2
     python3 $baseDir/scripts/xcor.py -t $seTagAlign
     """
   }
@@ -417,6 +472,7 @@ 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:
 
@@ -449,6 +505,29 @@ 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/experimentQC", mode: 'copy'
+
+  input:
+
+  file bigWigList from bigwigs.collect()
+
+  output:
+
+  file '*.{png,gz}' into plotProfile
+
+  when:
+
+  !skipPlotProfile
+
+  script:
+  """
+  module load deeptools/2.5.0.1
+  bash $baseDir/scripts/plot_profile.sh -g $gtfFile
+  """
+}
+
 // Calculate Consensus Peaks
 process consensusPeaks {
 
@@ -497,7 +576,7 @@ process peakAnnotation {
 
   """
   module load R/3.3.2-gccmkl
-  Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $genome
+  Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $gtfFile $geneNames
   """
 
 }
@@ -524,7 +603,9 @@ process motifSearch {
   script:
 
   """
-  module load R/3.3.2-gccmkl
+  module load python/3.6.1-2-anaconda
+  module load meme/4.11.1-gcc-openmpi
+  module load bedtools/2.26.0
   python3 $baseDir/scripts/motif_search.py -d $designMotifSearch -g $fasta -p $topPeakCount
   """
 }
@@ -559,15 +640,13 @@ process diffPeaks {
 
   """
   module load python/3.6.1-2-anaconda
-  module load meme/4.11.1-gcc-openmpi
-  module load bedtools/2.26.0
+  module load R/3.3.2-gccmkl
   Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
   """
 }
 
 // Generate Multiqc Report, gerernate Software Versions and references
 process multiqcReport {
-
   publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
@@ -600,11 +679,12 @@ process multiqcReport {
   """
   module load python/3.6.1-2-anaconda
   module load pandoc/2.7
-  module load multiqc/1.7
+  module load singularity/3.0.2
   echo $workflow.nextflow.version > version_nextflow.txt
-  multiqc --version > version_multiqc.txt
+  singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img 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 .
+  singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img multiqc -c $multiqc .
   """
 }

workflow/nextflow.config

@@ -4,11 +4,28 @@ profiles {
   }
 }
 
+trace {
+  enabled = true
+  file = 'pipeline_trace.txt'
+  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}
+
+timeline {
+  enabled = true
+  file = 'timeline.html'
+}
+
+report {
+  enabled = true
+  file = 'report.html'
+}
+
+
 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 = '1.1.2'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.31.0'
 }

workflow/scripts/annotate_peaks.R

 #!/bin/Rscript
 
-# Load libraries
-library("ChIPseeker")
-
-# Currently mouse or human
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+#* --------------------------------------------------------------------------
+#*
 
-library("TxDb.Hsapiens.UCSC.hg19.knownGene")
-library("TxDb.Mmusculus.UCSC.mm10.knownGene")
-library("TxDb.Hsapiens.UCSC.hg38.knownGene")
-library("org.Hs.eg.db")
-library("org.Mm.eg.db")
+#Currently Human or Mouse
 
+# Load libraries
+library("ChIPseeker")
+library(GenomicFeatures)
 
 # Create parser object
 args <- commandArgs(trailingOnly=TRUE)
 
 # Check input args
-if (length(args) != 2) {
-  stop("Usage: annotate_peaks.R annotate_design.tsv genome_assembly", call.=FALSE)
+if (length(args) != 3) {
+  stop("Usage: annotate_peaks.R annotate_design.tsv gtf geneNames", call.=FALSE)
 }
 
 design_file <- args[1]
-genome_assembly <- args[2]
+gtf <- args[2]
+geneNames <- args[3]
 
 # Load UCSC Known Genes
-if(genome_assembly=='GRCh37') {
-    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
-    annodb <- 'org.Hs.eg.db'
-} else if(genome_assembly=='GRCm38')  {
-    txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
-    annodb <- 'org.Mm.eg.db'
-} else if(genome_assembly=='GRCh38')  {
-    txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
-    annodb <- 'org.Hs.eg.db'
-}
+txdb <- makeTxDbFromGFF(gtf)
+sym <- read.table(geneNames, header=T, sep='\t') [,4:5]
 
 # Output version of ChIPseeker
 chipseeker_version = packageVersion('ChIPseeker')
@@ -48,18 +41,19 @@ names(files) <- design$Condition
 # Granges of files
 
 peaks <- lapply(files, readPeakFile, as = "GRanges", header = FALSE)
-peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
+peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb, tssRegion=c(-3000, 3000), verbose=FALSE)
 
-column_names <- c("chr", "start", "end", "width", "strand_1", "name", "score", "strand", "signalValue",
+column_names <- c("geneId","chr", "start", "end", "width", "strand_1", "name", "score", "strand", "signalValue",
                   "pValue", "qValue", "peak", "annotation", "geneChr", "geneStart", "geneEnd",
-                  "geneLength" ,"geneStrand", "geneId", "transcriptId", "distanceToTSS",
-                  "ENSEMBL", "symbol", "geneName")
+                  "geneLength" ,"geneStrand", "transcriptId", "distanceToTSS", "symbol")
 
 for(index in c(1:length(peakAnnoList))) {
   filename <- paste(names(peaks)[index], ".chipseeker_annotation.tsv", sep="")
   df <- as.data.frame(peakAnnoList[[index]])
-  colnames(df) <- column_names
-  write.table(df[ , !(names(df) %in% c('strand_1'))], filename, sep="\t" ,quote=F, row.names=F)
+  df$geneId <- sapply(strsplit(as.character(df$geneId), split = "\\."), "[[", 1)
+  df_final <- merge(df, sym, by.x="geneId", by.y="ensembl", all.x=T)
+  colnames(df_final) <- column_names
+  write.table(df_final[ , !(names(df_final) %in% c('strand_1'))], filename, sep="\t" ,quote=F, row.names=F)
 
   # Draw individual plots
 

workflow/scripts/call_peaks_macs.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate peaks from data.'''
 
 import os
@@ -132,8 +138,20 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
     with open(xcor, 'r') as xcor_fh:
         firstline = xcor_fh.readline()
         frag_lengths = firstline.split()[2]  # third column
-        fragment_length = frag_lengths.split(',')[0]  # grab first value
-        logger.info("Fraglen %s", fragment_length)
+        frag_lengths_array = frag_lengths.split(',')
+        fragment_length = 0
+        fragment = False
+        # Loop through all values of fragment length
+        for f in frag_lengths.split(','):
+            fragment_length = f
+            logger.info("Fraglen %s", fragment_length)
+            if int(fragment_length) > 50:
+                fragment = True
+                break
+
+        if fragment == False:
+            logger.info('Error in cross-correlation analysis: %s', frag_lengths_array)
+            raise Exception("Error in cross-correlation analysis: %s" % frag_lengths_array)
 
     # Generate narrow peaks and preliminary signal tracks
 

workflow/scripts/check_design.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Check if design file is correctly formatted and matches files list.'''
 
 import argparse

workflow/scripts/convert_reads.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Convert tagAlign files for further processing.'''
 
 import os

workflow/scripts/diff_peaks.R

 #!/bin/Rscript
 
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+#* --------------------------------------------------------------------------
+#*
+
 # Load libraries
 library("DiffBind")
 

workflow/scripts/experiment_design.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate experiment design files for downstream processing.'''
 
 import argparse

workflow/scripts/experiment_qc.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Experiment correlation and enrichment of reads over genome-wide bins.'''
 
 

workflow/scripts/generate_references.py

 #!/usr/bin/env python
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Make header for HTML of references.'''
 
 import argparse

workflow/scripts/generate_versions.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Make YAML of software versions.'''
 
 from __future__ import print_function
@@ -40,6 +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 (\S+)"],
     'MultiQC': ['version_multiqc.txt', r"multiqc, version (\S+)"],
 }
 
@@ -102,6 +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/map_qc.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Remove duplicates and filter unmapped reads.'''
 
 import os