Updated by Jelena - 14:00 16/Dec/2015

CC2 release - launched 10/Jun/2015

Bug fixes and updates in CCanalyser2.pl (after release) :

13/Dec/2015 Support fix - The data0 data area moved (and script stopped working). Now fixed - bigwig generation master file points to the new location.

24/Jul/2015 Bug fix - The pipeline didn't recognize --globin parameter. Now fixed.

11/Jun/2015 Bug fix - With James' words : "if the reporter read is sequenced with both PE1 and 2 when there is too little overlap to reconstruct the read into a single one". Added James' bug fix to this release.

Bug fixes and updates in Pipe2/pipe.sh (after release) :

15/Dec/2015 Bug fix - The rerun option --onlyCCanalyser was removing the "original run output" SAM file instead of using it in the re-run (typo in samtools view commmand). Now fixed.

Bug fixes and updates in Pipe1/pipe.sh (after release) :

04/Dec/2015 Improved feature - The pipeline didn't auto-generate SYMBOLIC LINKS to the bigwigs (but copied the bigwigs to public). Now auto-generates folder "PERMANENT_BIGWIGS_do_not_move" to run folder, thus avoiding clogging the /public/ area.

03/Dec/2015 Bug fix - The pipeline didn't auto-generate public folder "sample" for the data - risked overwrite if running multiple samples with same --pf parameter. Now fixed.