diff --git a/docs/references.md b/docs/references.md
index 6998a595fbf6d3a2d8c41be5eee62848bf1a5ef7..a5eba7df9025ddbd0ca98ee0a1b7c0e89f8c9f2d 100644
--- a/docs/references.md
+++ b/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)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 5d388c69fc692298fe86dc55e59498245812860b..6e2e885661a011956aaf1bac1e4fb0da3969d686 100644
--- a/workflow/conf/biohpc.config
+++ b/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'
}
}
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index cd40e9c54de736cbe4b198007e9089f1bf8a8ecb..bab17e5b675bc2ea8458f54cc3636b0c73f884f1 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/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: ''
diff --git a/workflow/main.nf b/workflow/main.nf
index 85cce33b1e724886f4bffebab2209d8533e03122..3045aaaf490f4449757823788d7066fae1822de9 100644
--- a/workflow/main.nf
+++ b/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 .
"""
}
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index f6d3f62d50df3244fb9b020c64800eba1042dfa2..661b266223b4c6974d368380f93c04c01a51c46c 100644
--- a/workflow/scripts/generate_versions.py
+++ b/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)
diff --git a/workflow/tests/test_generate_software_references.py b/workflow/tests/test_generate_software_references.py
index a627887eefe6359045abcefa54024f86e91d33d1..0235f2ed2a8502fba78437dc7ae03f3f38153dda 100644
--- a/workflow/tests/test_generate_software_references.py
+++ b/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
diff --git a/workflow/tests/test_generate_software_versions.py b/workflow/tests/test_generate_software_versions.py
index 276fc9681a61999d71f246495691853b48c7efa4..1048e490fae2bda3346f9f9783419633774846fa 100644
--- a/workflow/tests/test_generate_software_versions.py
+++ b/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