diff --git a/CHANGELOG.md b/CHANGELOG.md
index 963440e1d68fad9df897d8edd2f7740395d6e97a..5dfb5ee9e5b4161f287533be5ea9c83b5cdf3b74 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/README.md b/README.md
index 49057a8aa7e76c5635d1928eb62b7f9ae363cc18..99a5bd060bdddcb13603d487f34df85e52b2d3bd 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# **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)
diff --git a/docs/index.md b/docs/index.md
index d15742679154a8e3b95ca0fba9268787cd0831e6..18ae6ed89ce26535ecd5b055013b94c693706866 100644
--- a/docs/index.md
+++ b/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
diff --git a/docs/references.md b/docs/references.md
index 2ac5c0c3713c6f6a749a250bdb770bfbf21ca362..22ee1d655428b8017f25d96a63c409b61336a9da 100644
--- a/docs/references.md
+++ b/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)**.
diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index f71c26632674d2eab2c9a37dc7568c715e790543..e43a63c691584eb46f30e2a874dfe097fba17078 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/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
diff --git a/workflow/tests/test_generate_software_versions.py b/workflow/tests/test_generate_software_versions.py
index 77c674051476e707a8d5ab556d1c4ff498d8e94d..1eae5b852d5fef687a1ea22283e3a807f92960f2 100644
--- a/workflow/tests/test_generate_software_versions.py
+++ b/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