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