Merge branch '53-license' into 'master'

Resolve "Add license"

Closes #53

See merge request !47

.gitlab/merge_request_templates/merge_request.md

 
-Please fill in the appropriate checklist below (delete whatever is not relevant). 
+Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 ## PR checklist
@@ -8,4 +8,4 @@ These are the most common things requested on pull requests (PRs).
  - [ ] Documentation in `docs` is updated
  - [ ] `CHANGELOG.md` is updated
  - [ ] `README.md` is updated
-
+ - [ ] `LICENSE.md` is updated with new contributors

CHANGELOG.md

@@ -3,6 +3,8 @@
 All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
+### Added
+- MIT LICENSE
 
 ## [publish_1.0.5 ] - 2019-05-16
 ### Fixed

LICENSE.md

+MIT License
+
+Copyright (c) 2019, University of Texas Southwestern Medical Center.
+All rights reserved.
+Contributors: Spencer D. Barnes, Holly Ruess, Beibei Chen, Venkat S. Malladi
+Department: Bioinformatic Core Facility, Department of Bioinformatics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

docs/references.md

@@ -49,7 +49,7 @@
   * 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)
+  * 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_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)

docs/references.txt

-python/3.6.1-2-anaconda:
-Anaconda (Anaconda Software Distribution, https://anaconda.com)
-
-trimgalore/0.4.1:
-trimgalore/0.4.1 (https://github.com/FelixKrueger/TrimGalore)
-
-cutadapt/1.9.1:
-Marcel, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1):10-12. DOI: http://dx.doi.org/10.14806/ej.17.1.200
-
-bwa/intel/0.7.12:
-Li H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25: 1754-60. 
-
-samtools/1.6:
-Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9.
-
-sambamba/0.6.6:
-Tarasov, A., A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. 2015 Sambamba: fast processing of NGS alignment formats. Bioinformatics 31(12): 2032-2034. doi:10.1093/bioinformatics/btv098.
-
-bedtools/2.26.0:
-Quinlan, A. R., and I. M. Hall. 2010. BEDTools: a flexible suite of utilities for comparing genomic feautures. Bioinformatics 26(6): 841-842. doi:10.1093/bioinformatics/btq033
-
-deeptools/2.5.0.1:
-Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi: 10.1093/nar/gkw257.
-
-phantompeakqualtools/1.2:
-Landt S. G., G. K. Marinov, A. Kundaje, et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 9: 1813-31. doi: 10.1101/gr.136184.111.
-Kharchenko P. K., M. Y. Tolstorukov, and P. J. Park. 2008. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26(12): 1351-1359.
-
-macs/2.1.0-20151222:
-Zhang Y., T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson, B. E. Bernstein, C. Nusbaum, R. M. Myers, M. Brown, W. Li, and X. S. Liu. 2008. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
-
-UCSC_userApps/v317
-Kent W. J., A. S. Zweig, G. Barber, A. S. Hinrichs, and D. Karolchik. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics 26(17): 2204-2207.
-
-R/3.3.2-gccmkl:
-R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
-
-meme/4.11.1-gcc-openmpi:
-Bailey T. L., M. Bodén, F. A. Buske, M. Frith, C. E. Grant, L. Clementi, J. Ren, W. W. Li, and W. S. Noble. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research 37: W202-W208.
-Machanick P., and T. L. Bailey. 2011. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27(12): 1696-1697.
-
-R ChIPseeker:
-Yu G., L. Wang, and Q. He. 2015. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31(14): 2382-2383. doi: 10.1093/bioinformatics/btv145.
-
-R 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.
-
-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. http://www.nature.com/nature/journal/v481/n7381/full/nature10730.html.
-

workflow/conf/multiqc_config.yaml

+# Custom Logo
+custom_logo: 'bicf_logo.png'
+custom_logo_url: 'https://www.utsouthwestern.edu/labs/bioinformatics/'
+custom_logo_title: 'Bioinformatics Core Facility'
+
+report_header_info:
+    - Contact E-mail: 'bicf@utsouthwestern.edu'
+    - Application Type: 'ChIP-seq'
+    - Department: 'Bioinformatic Core Facility, Department of Bioinformatics'
+    - Contributors and Licensing: 'See https://doi.org/10.5281/zenodo.2648844'
+
+
 # Title to use for the report.
 title: BICF ChIP-seq Analysis Report
 

workflow/main.nf

 #!/usr/bin/env nextflow
 
+/*
+
+BICF ChIP-seq Analysis Workflow
+#### Homepage / Documentation
+https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/
+Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+
+
+*/
+
 // Path to an input file, or a pattern for multiple inputs
 // Note - $baseDir is the location of this workflow file main.nf
 

workflow/scripts/annotate_peaks.R

 #!/bin/Rscript
 
+/*
+ * --------------------------------------------------------------------------
+ * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+ * --------------------------------------------------------------------------
+ */
+
 # Load libraries
 library("ChIPseeker")
 

workflow/scripts/call_peaks_macs.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate peaks from data.'''
 
 import os

workflow/scripts/check_design.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Check if design file is correctly formatted and matches files list.'''
 
 import argparse

workflow/scripts/convert_reads.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Convert tagAlign files for further processing.'''
 
 import os

workflow/scripts/diff_peaks.R

 #!/bin/Rscript
 
+/*
+ * --------------------------------------------------------------------------
+ * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+ * --------------------------------------------------------------------------
+ */
+
 # Load libraries
 library("DiffBind")
 

workflow/scripts/experiment_design.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Generate experiment design files for downstream processing.'''
 
 import argparse

workflow/scripts/experiment_qc.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Experiment correlation and enrichment of reads over genome-wide bins.'''
 
 

workflow/scripts/generate_references.py

 #!/usr/bin/env python
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Make header for HTML of references.'''
 
 import argparse

workflow/scripts/generate_versions.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Make YAML of software versions.'''
 
 from __future__ import print_function

workflow/scripts/map_qc.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Remove duplicates and filter unmapped reads.'''
 
 import os

workflow/scripts/map_reads.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Align reads to reference genome.'''
 
 import os

workflow/scripts/motif_search.py

 #!/usr/bin/env python3
 
+#
+# * --------------------------------------------------------------------------
+# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+# * --------------------------------------------------------------------------
+#
+
 '''Call Motifs on called peaks.'''
 
 import os