diff --git a/CHANGELOG.md b/CHANGELOG.md
index f203c0a59fe0944ee6a9d81234c11be83791ccd0..e1398fc9d7414342848db2aaacece013598ca99e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,10 @@ All notable changes to this project will be documented in this file.
- Fix xcor to increase file size for --random-source
- Fix skip diff test for paired-end data
- Add test data for single control and single replicate
+- Fix python version for MultiQC report
+- Fix xcor to get lowest non zero value above 50
+- Fix references to display in Multiqc report
+
## [publish_1.0.6 ] - 2019-05-31
### Added
diff --git a/test_data/test_cross.qc b/test_data/test_cross.qc
new file mode 100644
index 0000000000000000000000000000000000000000..6fbc0ad1ab342196e525953dbcb28b6d07ba24f9
--- /dev/null
+++ b/test_data/test_cross.qc
@@ -0,0 +1 @@
+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
diff --git a/workflow/main.nf b/workflow/main.nf
index bf87941930e7a3737c8610703d224887c113a4d1..765ba3b1d1cd5b1d37d8dc339464d694c46ab8e2 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -654,10 +654,10 @@ process multiqcReport {
"""
echo $workflow.nextflow.version > version_nextflow.txt
- singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc.sif 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
- singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc.sif multiqc -c $multiqc .
+ singularity exec /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img multiqc -c $multiqc .
"""
}
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index e094fb914734cf66e7ec4b99be19511585c10e63..f7527ebffffd5b87860f736e6e5382f4ea886eb7 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -138,8 +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
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 4f0d8b143b36efbe207a303b2eb164d0de1a0e8a..c4814eda4cc375a5634f01ae7c4ff6f0b712a5ce 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -46,7 +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+)"],
+ 'Python': ['version_python.txt', r"Python (\S+)"],
'MultiQC': ['version_multiqc.txt', r"multiqc, version (\S+)"],
}
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index cd94e1783a25ffa953b3666f7cb3172c33f4f0bd..3b4404dfda2499cbb416e851bb7fcc3289d7de90 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -3,10 +3,29 @@
import pytest
import os
import utils
+from io import StringIO
+import call_peaks_macs
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/callPeaksMACS/'
+test_data_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../../test_data/'
+
+
+@pytest.mark.unit
+def test_fragment_length():
+ experiment = "experiment.tagAlign.gz"
+ control = "control.tagAlign.gz"
+ prefix = 'test'
+ genome_size = 'hs'
+ chrom_sizes = 'genomefile.txt'
+ cross_qc = os.path.join(test_data_path, 'test_cross.qc')
+ with pytest.raises(Exception) as excinfo:
+ call_peaks_macs.call_peaks_macs(experiment, cross_qc, control, prefix, genome_size, chrom_sizes)
+ assert str(excinfo.value) == "Error in cross-correlation analysis: ['0', '20', '33']"
+
+
@pytest.mark.singleend
def test_fc_signal_singleend():
diff --git a/workflow/tests/test_generate_software_references.py b/workflow/tests/test_generate_software_references.py
index 4d0025dfc3a925d2ec0d7bcd2bae86529d75e574..2420c6f3cee4032ea073219b7ada4a73b8582176 100644
--- a/workflow/tests/test_generate_software_references.py
+++ b/workflow/tests/test_generate_software_references.py
@@ -4,6 +4,7 @@ import pytest
import os
import utils
import yaml
+from bs4 import BeautifulSoup
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/multiqcReport/'
@@ -21,3 +22,14 @@ def test_software_references_output():
data_loaded = yaml.load(stream)
assert len(data_loaded['data'].split('<ul>')) == 19
+
+
+@pytest.mark.singleend
+def test_software_references_html():
+ multiqc_report = os.path.join(test_output_path, 'multiqc_report.html')
+ html_file = open(multiqc_report, 'r')
+ source_code = html_file.read()
+ multiqc_html = BeautifulSoup(source_code, 'html.parser')
+ references = multiqc_html.find(id="mqc-module-section-Software_References")
+ assert references is not None
+ assert len(references.find_all('ul')) == 18
diff --git a/workflow/tests/test_generate_software_versions.py b/workflow/tests/test_generate_software_versions.py
index 04ecdf3f57edee3507abaec27652023c8c5f5716..80b9981dabbf2c5944b74af792dae5a8621b6146 100644
--- a/workflow/tests/test_generate_software_versions.py
+++ b/workflow/tests/test_generate_software_versions.py
@@ -21,3 +21,4 @@ def test_software_versions_output():
data_loaded = yaml.load(stream)
assert len(data_loaded['data'].split('<dt>')) == 18
+ assert 'Not Run' not in data_loaded['data'].split('<dt>')[17]