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Commit f5301081 authored by Venkat Malladi's avatar Venkat Malladi
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Merge branch '52-outstading-bugs' into 'master'

Resolve "Astrocyte Bug Fixes"

Closes #52

See merge request BICF/Astrocyte/chipseq_analysis!46
parents a95135a2 fdd81bad
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......@@ -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
......
# **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)
......
......@@ -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
......
......@@ -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)**.
......@@ -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
......
......@@ -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
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