bug in order checking: first check if a project is in the restricted and then check if the project is on charon
added project name to error message
solved problem in conductor: not dealing properly with re-runs
commented part that was parsing all flowcell dir structure: saving more than 5 minutes per flowcellgit add ngi_pipeline/utils/parsers.pygit add ngi_pipeline/utils/parsers.py
added process single flowcell function to be sure to process a single flowcell per time
Conductor starts jobs on a flowcell per time and stores IDs into a local DB. On completion status is updated on Charon (still to be tested)
solved problem in Charon comunication in process_traking, wrong list of parameter and wrong return code
modify way in which db is returned in order to allow deletion of existing entries
started to work on updaiting charon at seq run level: only testing connection and getting run id.... I am going nuts here
script to clean charon at seq run level
pipeline now updates seq run once the alignment is done
now the total autosomal coverage is updated at sample level every time the run autosomal level is updated. in the future an API will do this
the pipeline to execute is now retrived from Charon
close to be ready versionof the pipeline
working version: pipeline + charon + piper
BugFix: before starting a new piper instance at sample level ngi_pipeline checks if that sample has been already processed or if it is currently under evaluation
removed testing code spotter by guillermo and added info message about sample being succesfully analysed by piper
Merge pull request #42 from vezzi/devel

NGI_pipeline working version