Add output prefix

[talnor]

Description

The features of this PR primarily concerns internals

Summary of the changes made:

• Output files for delivery are named with sample ID
• Paths in deliverables file updated and changed accordingly

If not self-evident, mention what prompted the change.

• Files in housekeeper need unique names

Primary function of PR

• [ ] Hotfix
• [x] Patch
• [ ] Minor functionality improvement
• [ ] New type of analysis
• [ ] Backward-breaking functionality improvement
• [ ] This change requires internal documents to be updated
• [ ] This change requires another repository to be updated

Testing

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh add_output_prefix

• us

• source activate S_microSALT

• microSALT analyse /home/proj/stage/microbial/queries/ACC5551.json --input /home/proj/stage/microbial/fastq/ACC5551

• microSALT analyse /home/proj/stage/microbial/queries/ACC5551A1.json --input /home/proj/stage/microbial/fastq/ACC5551/ACC5551A1

• Ensure there are no errors when running the analysis

• Verify that all files specified in the deliverables file exist

Test results

Paths in deliverables files exists and contain sample ID. No unexpected errors

Exceptions are samples that (as expected) failed the analysis, i.e. NTC and low quality samples. Is missing data handled at a later step as for MIP?

Sign-offs

• [X] Code tested by @talnor
• [X] Approved to run at Clinical-Genomics by @sylvinite

[talnor]

Results of testing PR:

Paths in deliverables files exists and contain sample ID. No unexpected errors

Exceptions are samples that (as expected) failed the analysis, i.e. NTC and low quality samples. Is missing data handled at a later step as for MIP?