Merge branch '52-outstading-bugs' into 'master'

Resolve "Astrocyte Bug Fixes"

Closes #52

See merge request BICF/Astrocyte/chipseq_analysis!46

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
-## [publish_1.0.4 ] - 2019-05-15
+## [publish_1.0.5 ] - 2019-05-16
 ### Fixed
 - Retitled documentation for skipDiff and skipMotif to be more clear
 - Add missing python module for motif search

README.md

 # **CHIPseq Manual**
-## Version 1.0.0
-## May 2, 2019
+## Version 1.0.5
+## May 16, 2019
 
 # BICF ChIP-seq Pipeline
 
@@ -19,7 +19,7 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
 
 This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://portal.biohpc.swmed.edu/content/). However, the pipeline should be able to run on any system that supports Nextflow.
 
-Additionally, the pipeline is designed to work with [Astrocyte Workflow System](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html) using a simple web interface.
+Additionally, the pipeline is designed to work with [Astrocyte Workflow System](https://astrocyte.biohpc.swmed.edu/static/docs/index.html) using a simple web interface.
 
 Current version of the software and issue reports are at
 https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis
@@ -130,7 +130,7 @@ diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks
 If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know and we will add it here.
 
 ## Citation
-Please cite individual programs and versions used [HERE](docs/references.txt). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596). Also, please look out for our pipeline to be published in the future [HERE](https://zenodo.org/).
+Please cite individual programs and versions used [HERE](docs/references.txt), and the pipeline doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
 
 ## Programs and Versions
   + python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.txt)

docs/index.md

@@ -72,7 +72,7 @@ experimentQC | heatmeap_SpearmanCorr.pdf | plot of Spearman correlation between
 experimentQC | heatmeap_PearsonCorr.pdf | plot of Pearson correlation between samples
 experimentQC | sample_mbs.npz | array of multiple BAM summaries
 crossReads | *.cc.plot.pdf | Plot of cross-correlation to assess signal-to-noise ratios
-crossReads | *.cc.qc | cross-correlation metrics. File [HEADER](docs/xcor_header.txt)
+crossReads | *.cc.qc | cross-correlation metrics. File [HEADER](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/xcor_header.txt)
 callPeaksMACS | pooled/*pooled.fc_signal.bw | bigwig data file; raw fold enrichment of sample/control
 callPeaksMACS | pooled/*pooled_peaks.xls | Excel file of peaks
 callPeaksMACS | pooled/*.pvalue_signal.bw | bigwig data file; sample/control signal adjusted for pvalue significance

docs/references.md

@@ -52,6 +52,6 @@
   * 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)
 
 17. **BICF ChIP-seq Analysis Workflow**:
-  * Spencer D. Barnes, Holly Ruess, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.4). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
+  * Spencer D. Barnes, Holly Ruess, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
 
 Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.

workflow/tests/test_annotate_peaks.py

@@ -24,7 +24,7 @@ def test_upsetplot_singleend():
 def test_annotation_singleend():
     annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 149284
+    assert utils.count_lines(annotation_file) >= 149284
 
 
 @pytest.mark.pairedend

workflow/tests/test_generate_software_versions.py

@@ -20,4 +20,4 @@ def test_software_versions_output():
     with open(software_versions, 'r') as stream:
         data_loaded = yaml.load(stream)
 
-    assert len(data_loaded['data'].split('<dt>')) == 17
+    assert  len(data_loaded['data'].split('<ul>')) == 18