Contamination

[sylvinite]

Description

The features of this PR primarily concerns end-users & bioinformaticians

This is a summary of the changes made.

• [ ] Contamination check added to QC, and visible in QC report
• [ ] Contamination utils command to easily check contamination levels post-analysis
• [ ] Duplication indicator (based on typing)
• [x] Added contamination threshold to config

This is list of necessary subtasks:

• [ ] Kontakta KS för att validera även under KS
• [ ] Skriv valideringsrapport
• [ ] Skriv implementationsplan
• [ ] Dubbelkolla att versionnummer uppdateras korrekt när kontamineringsdatabas ger nytt resultat
• [ ] Skriv självtest
• [ ] Korrekt flagga prover som kontaminerade/icke-kontaminerade
• [ ] Skriv contig tröskelvärde baserat på CLC resultat
• [ ] Ta fram o spara inputdata för kont/icke-kont baserat på CLC data
• [ ] Sammanställ kont/icke-kont baserat på CLC resultat [kan fragmenteras]
• [ ] Skriv QC-rapport uppdatering som skriver ut svar i report
• [ ] Skriv skrapare som laddar upp blast/kraken i databas
• [ ] Specca exakt vad som ska synas i rapport
• [ ] Skriv referencer som håller databasen uppdaterad
• [ ] Skriv job_creator som startar BLAST på contigs mot refset/nt/
• [ ] Skriv job_creator som startar Kraken på reads mot krakendatabas
• [ ] Välj databas att kontamineringschecka emot
• [ ] Välj blast/kraken att använda för kontaminering/duplikation

Primary function of PR

• [ ] Hotfix
• [ ] Patch
• [ ] Minor functionality improvement
• [X] 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

This is a description of the tests necessary to verify the stability of the PR.

Basic test routine:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh BRANCHNAME
• us
• _source activate S_microSALT_
• _(SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json_
• Select a relevant subset of the following:
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109
• microSALT analyse project ACC5551

_Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx

New analysis test routine: The new analysis (contamination) is tested as follows:

• Samples with known duplicates are evaluated
• Samples with contamination issues according to CLC are evaluated
• Samples with no know contamination issues are evaluated according to species, and % of contamination

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

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