Merge pull request #48 from StevenWingett/development

Development

Author: StevenWingett

.gitignore

@@ -0,0 +1,39 @@
+!Build/
+.last_cover_stats
+/META.yml
+/META.json
+/MYMETA.*
+*.o
+*.pm.tdy
+*.bs
+
+# Devel::Cover
+cover_db/
+
+# Devel::NYTProf
+nytprof.out
+
+# Dizt::Zilla
+/.build/
+
+# Module::Build
+_build/
+Build
+Build.bat
+
+# Module::Install
+inc/
+
+# ExtUtils::MakeMaker
+/blib/
+/_eumm/
+/*.gz
+/Makefile
+/Makefile.old
+/MANIFEST.bak
+/pm_to_blib
+/*.zip
+
+# Additionals (not necessarily Perl-related)
+.Rhistory
+.DS_Store

Misc/remove_tags.pl

@@ -10,9 +10,9 @@
 ###########################################################################
 ###########################################################################
 ##                                                                       ##
-## Copyright 2021, Simon Andrews    ([email protected])       ##
-##                 Steven Wingett   ([email protected])      ##
-##                 Felix Krueger    ([email protected])       ##
+## Copyright 2022, Simon Andrews    (The Babraham Institute, UK)         ##
+##                 Steven Wingett   (MRC-LMB, Cambridge, UK)             ##
+##                 Felix Krueger    (The Babraham Institute UK)          ##
 ##                 Mark Fiers       (Plant & Food Research, NZ)          ##
 ##                                                                       ##
 ## This program is free software: you can redistribute it and/or modify  ##

README.txt

@@ -18,5 +18,3 @@ https://github.com/StevenWingett/FastQ-Screen
 
 Bug reports, queries or suggestions can be made at:
 https://github.com/StevenWingett/FastQ-Screen/issues
-
-Alternatively, please email [email protected]

RELEASE_NOTES.txt

@@ -1,12 +1,6 @@
-Release notes for FastQ Screen v0.15.0 (12 October 2021)
-----------------------------------------------------------
-Added remove_tags.pl in new Misc folder. This script
-removes FastQ Screen genome filter tags from read headers, 
-which may be necessary for downstream analysis.
-
-Downloading test genomes with wget now executed with 
---no-check-certificate parameter, to prevent downloading 
-failures on some systems.  
+Release notes for FastQ Screen v0.15.1 (11 January 2022)
+--------------------------------------------------------
+Updated contact details. 
 
 
 

fastq_screen

@@ -13,14 +13,14 @@ use File::Path;
 use Data::Dumper;
 
 
-our $VERSION = "0.15.0";
+our $VERSION = "0.15.1";
 
 ###########################################################################
 ###########################################################################
 ##                                                                       ##
-## Copyright 2021, Simon Andrews    ([email protected])       ##
-##                 Steven Wingett   ([email protected])      ##
-##                 Felix Krueger    ([email protected])       ##
+## Copyright 2022, Simon Andrews    (The Babraham Institute, UK)         ##
+##                 Steven Wingett   (MRC-LMB, Cambridge, UK)             ##
+##                 Felix Krueger    (The Babraham Institute UK)          ##
 ##                 Mark Fiers       (Plant & Food Research, NZ)          ##
 ##                                                                       ##
 ## This program is free software: you can redistribute it and/or modify  ##
@@ -2489,7 +2489,6 @@ __DATA__
 FastQ Screen - Map sequences against multiple genomes
 
 www.bioinformatics.babraham.ac.uk/projects/fastq_screen
-Contact: [email protected]
 
 Synopsis
 

fastq_screen_documentation.md

@@ -292,8 +292,8 @@ Terms of use
 FastQ Screen is distributed under a "GNU General Public License", a copy of which is distributed with the software.
 
 
-Papers citing FastQ Screen
-==========================
+Selected Papers citing FastQ Screen
+===================================
 Picornell AC, Echavarria I, Alvarez E, et al.: Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series. BMC Genomics. 2019; DOI: 10.1186/s12864-019-5849-0
 
 Laufer BI, Hwang H, Vogel Ciernia A et al., Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights. Epigenetics. 2019; 14(7), 672-684; DOI:10.1080/15592294.2019.1609867
@@ -326,5 +326,3 @@ Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and qual
 Report problems
 ===============
 If you have any problems running this program you can report them on `GitHub <https://github.com/StevenWingett/FastQ-Screen/issues>`_.
-
-Please email any other queries to: [email protected]