Add in multiqc reports.

docs/references.md

@@ -47,3 +47,6 @@
 15. **DiffBind**:
   * Stark R., and G. Brown. 2011. DiffBind: differential binding analysis of ChIP-Seq peak data. [http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf](http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf). doi:[10.18129/B9.bioc.DiffBind](https://dx.doi.org/10.18129/B9.bioc.DiffBind)
   * Ross-Innes C. S., R. Stark, A. E. Teschendorff, K. A. Holmes, H. R. Ali, M. J. Dunning,  G. D. Brown, O. Gojis, I. O. Ellis, A. R. Green, S. Ali, S. Chin, C. Palmieri, C. Caldas, and J. S. Carroll. 2012. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481: 389-393. doi:[10.1038/nature10730](https://dx.doi.org/10.1038/nature10730)
+
+16. **MultiQc**:
+  * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354 ](https://dx.doi.org/10.1093/bioinformatics/btw354)

workflow/conf/biohpc.config

@@ -60,8 +60,8 @@ process {
     module = ['python/3.6.1-2-anaconda', 'meme/4.11.1-gcc-openmpi', 'bedtools/2.26.0']
     cpus = 32
   }
-  withName: softwareReport {
-    module = ['python/3.6.1-2-anaconda', 'pandoc/2.7']
+  withName: multiqcReport {
+    module = ['python/3.6.1-2-anaconda', 'pandoc/2.7', 'multiqc/1.7']
     executor = 'local'
   }
 }

workflow/conf/multiqc_config.yaml

@@ -2,36 +2,96 @@
 title: BICF ChIP-seq Analysis Report
 
 report_comment: >
-    This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/" target="_blank">BICF/chipseq_analysis</a>
-    pipeline.
-
-report_section_order:
-    software_versions:
-        order: -1000
-
-report_section_order:
-    software_references:
-        order: -1000
-
+  This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/" target="_blank">BICF/chipseq_analysis</a>
+  pipeline.
 
 extra_fn_clean_exts:
-    - '_R1'
-    - '_R2'
-    - 'pbc.qc'
+  - 'pbc.qc'
+  - 'cc.qc'
 
 fn_ignore_files:
-    - '*dedup.flagstat.qc'
+  - '*dedup.flagstat.qc'
 
 custom_data:
-    library_complexity:
-      file_format: 'tsv'
-      id: 'library_complexity'
-      contents: 'TotalReadPairs  DistinctReadPairs       OneReadPair     TwoReadPairs    NRF     PBC1    PBC2'
-      section_name: 'Library complexity'
-      plot_type: 'generalstats'
+  library_complexity:
+    file_format: 'tsv'
+    id: 'library_complexity'
+    contents: 'TotalReadPairs  DistinctReadPairs       OneReadPair     TwoReadPairs    NRF     PBC1    PBC2'
+    section_name: 'Library complexity'
+    plot_type: 'generalstats'
+    pconfig:
+        TotalReadPairs:
+          decimalPlaces: 0
+          shared_key: read_count
+        DistinctReadPairs:
+          decimalPlaces: 0
+          shared_key: read_count
+        NRF:
+          decimalPlaces: 2
+        PBC1:
+          decimalPlaces: 2
+        PBC2:
+          decimalPlaces: 2
 
 sp:
     phantompeakqualtools/out:
-        fn: '*cc.qc'
+      fn: '*cc.qc'
+    library_complexity:
+      fn: '*pbc.qc'
+    macs2:
+      fn: '*_peaks.xls'
+
+
+report_section_order:
+    cutadapt:
+      order: -1000
+    Samtools:
+      order: -1100
+    Software_Versions:
+      order: -1200
+    Software_References:
+      order: -1300
+
+table_columns_placement:
     library_complexity:
-        fn: '*pbc.qc'
+      TotalReadPairs: 1100
+      DistinctReadPairs: 1200
+      NRF: 1300
+      PBC1: 1400
+      PBC2: 1500
+    phantompeakqualtools:
+      Estimated_Fragment_Length_bp: 1600
+      NSC: 1700
+      RSC: 1800
+
+table_columns_visible:
+  cutadapt:
+    percent_trimmed: False
+  library_complexity:
+    OneReadPair: False
+    TwoReadPairs: False
+
+table_cond_formatting_rules:
+    library_complexity_mqc-generalstats-library_complexity-NRF:
+      pass:
+        - gt: 0.8
+      warn:
+        - lt: 0.8
+      fail:
+        - lt: 0.5
+    library_complexity_mqc-generalstats-library_complexity-PBC1:
+      pass:
+        - gt: 0.8
+      warn:
+        - lt: 0.8
+      fail:
+        - lt: 0.5
+    library_complexity_mqc-generalstats-library_complexity-PBC2:
+      pass:
+        - gt: 3
+      warn:
+        - lt: 3
+      fail:
+        - lt: 1
+
+thousandsSep_format: ''

workflow/main.nf

@@ -16,6 +16,7 @@ params.astrocyte = 'false'
 params.skipDiff = false
 params.skipMotif = false
 params.references = "$baseDir/../docs/references.md"
+params.multiqc =  "$baseDir/conf/multiqc_config.yaml"
 
 // Assign variables if astrocyte
 if (params.astrocyte) {
@@ -67,6 +68,7 @@ topPeakCount = params.topPeakCount
 skipDiff = params.skipDiff
 skipMotif = params.skipMotif
 references = params.references
+multiqc = params.multiqc
 
 if (params.pairedEnd == 'false'){
   pairedEnd = false
@@ -563,35 +565,46 @@ process diffPeaks {
   """
 }
 
-// Collect Software Versions and references
-process softwareReport {
+// Generate Multiqc Report, gerernate Software Versions and references
+process multiqcReport {
 
   publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
-    file ('trimReads_vf/*') from trimReadsVersions.first()
-    file ('alignReads_vf/*') from alignReadsVersions.first()
-    file ('filterReads_vf/*') from filterReadsVersions.first()
-    file ('convertReads_vf/*') from convertReadsVersions.first()
-    file ('crossReads_vf/*') from crossReadsVersions.first()
-    file ('callPeaksMACS_vf/*') from callPeaksMACSVersions.first()
-    file ('consensusPeaks_vf/*') from consensusPeaksVersions.first()
-    file ('peakAnnotation_vf/*') from peakAnnotationVersions.first()
-    file ('motifSearch_vf/*') from motifSearchVersions.first().ifEmpty()
-    file ('diffPeaks_vf/*') from diffPeaksVersions.first().ifEmpty()
-    file ('experimentQC_vf/*') from experimentQCVersions.first()
+  file ('trimReads_vf/*') from trimReadsVersions.first()
+  file ('alignReads_vf/*') from alignReadsVersions.first()
+  file ('filterReads_vf/*') from filterReadsVersions.first()
+  file ('convertReads_vf/*') from convertReadsVersions.first()
+  file ('crossReads_vf/*') from crossReadsVersions.first()
+  file ('callPeaksMACS_vf/*') from callPeaksMACSVersions.first()
+  file ('consensusPeaks_vf/*') from consensusPeaksVersions.first()
+  file ('peakAnnotation_vf/*') from peakAnnotationVersions.first()
+  file ('motifSearch_vf/*') from motifSearchVersions.first().ifEmpty()
+  file ('diffPeaks_vf/*') from diffPeaksVersions.first().ifEmpty()
+  file ('experimentQC_vf/*') from experimentQCVersions.first()
+  file ('trimReads/*') from trimgaloreResults.collect()
+  file ('alignReads/*') from mappedReadsStats.collect()
+  file ('filterReads/*') from dedupReadsComplexity.collect()
+  file ('crossReads/*') from crossReadsStats.collect()
 
   output:
 
   file('software_versions_mqc.yaml') into softwareVersions
   file('software_references_mqc.yaml') into softwareReferences
+  file "multiqc_report.html" into multiqcReport
+  file "*_data" in multiqcData
 
   script:
 
   """
+  module load python/3.6.1-2-anaconda
+  module load pandoc/2.7
+  module load multiqc/1.7
   echo $workflow.nextflow.version > version_nextflow.txt
+  multiqc --version > version_multiqc.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/scripts/generate_versions.py

@@ -40,6 +40,7 @@ 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+)"],
+    'MultiQC': ['version_multiqc.txt', r"multiqc, version (\S+)"],
 }
 
 
@@ -100,6 +101,7 @@ def main():
     results['MEME-ChIP'] = '<span style="color:#999999;\">Not Run</span>'
     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>'
 
     # list all files
     files = glob.glob('**/*.txt', recursive=True)

workflow/tests/test_generate_software_references.py

@@ -6,7 +6,7 @@ import utils
 import yaml
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/softwareReport/'
+                '/../output/multiqcReport/'
 
 
 @pytest.mark.singleend

workflow/tests/test_generate_software_versions.py

@@ -6,7 +6,7 @@ import utils
 import yaml
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/softwareReport/'
+                '/../output/multiqcReport/'
 
 
 @pytest.mark.singleend