Merge pull request #266 from martinghunt/pipeline

Fix typo so that adapter trimming gets run
Merge pull request #267 from martinghunt/pipeline

Fix so adapter trimming happens with IVA
Corrected the file names

This should fix th behaviour described on the RT ticket 390430
Corrected the filenames specified on RT ticket 390430
Merge branch 'no_rna_seq' of https://github.com/js21/vr-codebase into no_rna_seq
Merge pull request #268 from js21/no_rna_seq

Corected filenames for db update and clean up
Filenames now changed properly
Merge pull request #269 from js21/no_rna_seq

Filenames now changed properly. All tested.
filter PF fail reads and secondary alignments
filter secondarys at the end
esqcape out awk variables
reheader bam
dont overwrite input file as you read it
regenerate bamcheck file so the number of reads matches filtered bam
Merge pull request #270 from andrewjpage/import_read_filtering

Import read filtering
initial moving assembly files to prefixed directories
wrong output variable name
limit to a single lane
remove tmp directory before starting
pool fastqs done file in the lane root