Fix merge conflicts

CHANGELOG.md

@@ -7,6 +7,9 @@ All notable changes to this project will be documented in this file.
 - Add Nextflow to references.md
 - Fix pool_and_psuedoreplicate.py to run single experiment
 - Add test data
+- Add PlotProfile Option
+- Add Python version to MultiQC
+- Add and Update tests
 
 ## [publish_1.0.6 ] - 2019-05-31
 ### Added

README.md

@@ -116,6 +116,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
 diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
 diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
 diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
+plotProfile | plotProfile.png | Plot profile of the TSS region
+plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
 
 ## Common Quality Control Metrics
   + These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.

docs/index.md

@@ -90,6 +90,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
 diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
 diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
 diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
+plotProfile | plotProfile.png | Plot profile of the TSS region
+plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
 
 ## Common Quality Control Metrics
   + These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.

workflow/conf/biohpc.config

@@ -78,21 +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'
+      gtf = '/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'
+      gtf = '/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'
+      gtf = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
     }
   }
 }

workflow/main.nf

@@ -28,7 +28,6 @@ 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) {
@@ -37,6 +36,7 @@ if (params.astrocyte) {
   params.bwaIndex = "$referenceLocation/$params.genome"
   params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
   params.fasta = "$referenceLocation/$params.genome/genome.fa"
+  params.gtf = "$referenceLocation/$params.genome/gencode.gtf"
   if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
     params.genomeSize = 'hs'
   } else if (params.genome == 'GRCm38') {
@@ -47,6 +47,7 @@ if (params.astrocyte) {
     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 ].fasta ?: false : false
 }
 
 
@@ -463,13 +464,17 @@ peaksDesign = experimentPeaks
 
 //plotProfile
 process plotProfile {
-  publishDir "$outDir/${task.process}", mode: 'copy'
+  publishDir "$outDir/experimentQC", mode: 'copy'
 
   input:
 
   file ("*.pooled.fc_signal.bw") from bigwigs.collect()
   file gtf from gtfFile
 
+  output:
+
+  file '*.{png,gz}' into plotProfile
+
   when:
 
   !skipPlotProfile

workflow/scripts/plotProfile.sh

 #!/bin/bash
 #plotProfile.sh
 
-bws=`ls *.bw`
-gtf=`ls *.gtf *.bed`
+bws=$(ls *.bw)
+gtf=$(ls *.gtf *.bed)
 
 computeMatrix reference-point \
 	--referencePoint TSS \

workflow/tests/test_plot_profile.py

+#!/usr/bin/env python3
+
+import pytest
+import os
+import utils
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/experimentQC/'
+
+
+@pytest.mark.singleend
+def test_plot_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'plotProfile.png'))
+
+
+@pytest.mark.pairedend
+def test_plot_pairedend():
+    assert os.path.exists(os.path.join(test_output_path, 'computeMatrix.gz'))