rki output and some smaller fixes

[replikation]

• rki style output branch

Missing:

• pangolin lineage in rki csv
• collect fastas into multifasta for rki

[replikation]

@hoelzer apparently rki does not have a "pangolin" field... so I skip adding this

[hoelzer]

@hoelzer apparently rki does not have a "pangolin" field... so I skip adding this

@replikation what do you mean by "does not have a pangolin" field? The current DESH upload portal? No, currently there is no field to put the pangolin lineage.

[replikation]

@hoelzer yep DESH upload.

[hoelzer]

@hoelzer yep DESH upload.

Yeah, this is the first very very basic form for the first days (phase 0, https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/DESH/DESH.html) and will be subject to change. So we just need to adjust the output format following changes to the upload portal in the next days/weeks

[replikation]

yep we need to do this either way as we are sequencing every week now

[replikation]

• @hoelzer cleaned up output structure and added a combined fasta for the --rki flag
• html output not in here ill do a separate PR for this

[replikation]

• coul improve the "fastq collection" via find for the barcode dirs. then it would be "more" recursive stable...?

[replikation]

• PR closes allow input of a "raw basecalled fastq" dir #26 rki conform metadata output #27 Generate one summary consensus QC TSV #19

[hoelzer]

taxon,lineage,probability,pangoLEARN_version,status,note
FAO96286_barcode07,B.1.177,1.0,2021-01-11,passed_qc,

@replikation the column headers are not correct, or? First column is the sample or FASTA ID and not the taxon? Or is this just default pangolin output style (then let's keep it)

[replikation]

• @hoelzer oh good find, this is from my "collect all pangolin report part" here, so it can be manually changed

[hoelzer]

@replikation fine on my side! Nothing burned down :D checked on laptop and cluster and also with the new --fastq_raw option.

The comment above regarding lineage output is just minor

UPDATE: ah nice, then now everything fine! :)