Use bin and data directory heirarchy
added parameters for indatadir, outdatadir, reposdir, tmpdir and amended file nodes to use them.

Unless components of path to transcriptome are given as parameters, the --transcriptome-index flag for the tophat2 command will not be used
enhancements to handling substitutions in array refs
Merge pull request #2 from dozy/devel

Devel
added production of bamcheck, flagstat and cram files
updated format of some file nodes
Merge pull request #3 from dozy/devel

added production of bamcheck, flagstat and cram files
Merge branch 'devel' of https://github.com/dkj/p4 into dkj-devel
Merge branch 'dkj-devel' into devel
add colour for new VTFILE node type
add cfg name to document title
Merge pull request #4 from dozy/devel

add colour for new VTFILE node type; add cfg name to document title
Merge pull request #1 from wtsi-npg/devel

Devel
Create bai and md5 files, and save bed files
Add prefix to bed files
Change '.bed' filenames from optional with defaults to hard-coded
Merge pull request #5 from jenniferliddle/devel

Create bai and md5 files, and save bed files
Added library_type param, changed default name of target_bam file, added alignment_filter_jar_path paramater
Merge pull request #6 from jenniferliddle/devel

Added library_type param, changed default name of target_bam file, added...
changes target filename from _aln.bam to .bam
Merge pull request #7 from jenniferliddle/devel

changes target filename from _aln.bam to .bam
Ensure markdup report for phix does not clash with main markdup report