Hi guys!

Great work addressing this issue. There is a reason not to sync directly
from the archive folder if we want to deliver files (and we will) that have
been processed by the pipeline in some way (e.g. merged or adapter-trimmed
etc.). Another reason is that we can view the data under archive as only
temporarily available and we don't have a routine for ascertaining that a
sample has been delivered before removing the data from archive (which we
have for the data under nobackup/illumina). Bear in mind that with the next
version of the pipeline, we shouldn't have to unzip the input files, so I
don't expect this to be an issue anymore.




On Wed, Apr 30, 2014 at 12:44 PM, senthil10 <notifications@github.com>wrote:

> In scilifelab/pm/core/deliver.py:
>
> >      def _save(self, con, obj):
> >          """Dry-run aware wrapper around statusdb save
> >          """
> >          def runpipe():
> >              con.save(obj)
> >          return self.app.cmd.dry("storing object {} in {}".format(obj.get('_id'),con.db), runpipe)
> > -
> > +
> > +    def _find_uncompressed_fastq_files(self, proj_base_dir, samples):
> > +        """Finds samples with uncompressed fastq files in project/fc_id/sample_id directories
> > +        Returns a list of sample names
> > +        """
> > +
> > +        uncompressed = []
> > +        for sample in samples:
> > +            date = sample.get("date",False)
> > +            fcid = sample.get("flowcell",False)
> > +            dname = sample.get("barcode_name",False)
>
> @remiolsen <https://github.com/remiolsen> : I agree too [image: :+1:] may
> be we should take this to @b97pla <https://github.com/b97pla> and see
> what he thinks about it. Copying file from archive would be more easier and
> robust.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/SciLifeLab/scilifelab/pull/372/files#r12137638>
> .
>



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Pontus Larsson, PhD
Science For Life Laboratory
www.scilifelab.se

Email: Pontus.Larsson@scilifelab.se
Phone: +46 8 5248 1440
Mobile: +46 76 946 9788
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