Version 0.3.0

• Fix #21 - sort index file lines when grouping paired FASTQ files
• Disable Docker by default and update test script - resolve #22
• Update test profiles and main config - address #25
• Move process resource to external config file - #24
• Modified quantification step by removing the temporary sorted bam file. By doing this we can pipe an uncompressed sam file directly to rsem - #26 thanks @karl616
• Fix issue with modified quantification templates - introduced by #26
• Use withName process selector in configuration files - close #39
• Update test script, configuration profiles and checksums - #30
• Add option to enforce strandness - first implementation of #11
• Fix bedgraph filename error in contig template - close #27
• Add tool versions to readme - close #18

Additional fixes and imporvements:

• Change README markup to Markdown
• Update CI configuration
• Improve RGCRG bigwig templates by removing temporary bam files
• Fix missing NH:1 filter in contigs antisense template
• Move to Travis CI
• Fix issue with test script using wrong pipeline.db when running outside pipeline base dir

Full Changelog: v0.2.1...v0.3.0