Patch for moving runfolders

This version adds a patch that introduces the ability to configure the user and keyfile to use when doing the remote mv action for moving runfolders from incoming to runfolders.

New delivery workflows, setting charon status and moving runfolders on run completion

This version introduces a number of changes, most of which concern the delivery workflows.

• This brings arteria-packs up to date with arteria-delivery 2.0.0. This introduces a new way in which deliveries are handled, where a delivery artifact can only be delivered once. Re-delivering will require a force_delivery flag to be set.
• It introduces a new workflow delivery_runfolders_for_project_workflow, which will deliver a set of runfolders associated with a project. This workflow has multiple delivery modes CLEAN, BATCH or FORCE. CLEAN is the default mode, and assumes that this project has not been delivered before. If a project has multiple delivery instances BATCH can be used to indicate this. If this flag is used only runfolders which have not already been delivered will be delivered. Finally FORCE can be used to trigger a delivery of all runfolders for that project, whether they have been delivered before or not.
• For project deliveries the workflow will now update the charon delivery status
• Introducing a new sensor, which will look for runfolders and move them out of the folder to which the sequencing instruments writes once sequencing has finished. This is done to limit the exposure of data to the sequencing instrument computers after a run has finished.

v2.9.1-rc3: Merge pull request #78 from johandahlberg/default_set_charon_true

Default to setting delivery status in charon

v2.9.1-rc2: Merge pull request #77 from johandahlberg/default_to_set_charon_false

Set charon sample status setting to false by default

v2.9.1-rc1: Merge pull request #76 from johandahlberg/set_charon_status

Set delivery status in charon for BP samples

Minor update to deliver runfolder workflow

This includes a small feature to the deliver runfolder workflow such that we will only search for PI emails corresponding to the provided project names.

API tokens, SSL verification, and utility scripts

This release

• hides sensitive API tokens from the executions output
• requires the NGI UU workflow to verify Irma SSL certs
• adds utility script runfolder_search.py and modifies trace_runfolder.py so that it outputs all workflows matching the runfolder/trace tag

Delivery workflow updates and new minor features

As of this release it is possible to restrict which projects are delivered from a flowcell in the runfolder delivery workflow. In addition to this:

• the mover delivery id will show up in the delivery action output, making debugging easier
• when workflows are listed using the trace_runfolder.py script they will appear ordered by date

Include whether sensitive data is delivered

This release introduces an update to the runfolder/project delivery workflows that includes information to SUPR whether or not the specified data in the delivery project is sensitive or not.

Rollback ConversionStats workaround

Minor release that removes the ConversionStats workaround as the bug has now been fixed in the later versions of bcl2fastq.