Ensure all currently needed covsonar 1 commands are present in covsonar 2 and how to switch is documented

[matthuska]

The following covsonar 1 commands are commonly used and need to be supported by covsonar 2 if we are going to transition to using it. To be marked as completed, the command needs to be tested to ensure that it is working, and also it needs to be documented in the covsonar 2 README under the "Switching from covsonar 1" section.

general

• [x] create a database
• [x] update pangolin lineage parent-child relationships (alias.json)

autopilot

• [x] ./sonar.py add --noprogress --force --db $db --file $(realpath !{sequences}) --cpus !{task.cpus} #--cache \$TMPDIR
• [x] /sonar.py update --fields accession=covv_accession_id software=covv_assembly_method lineage=covv_lineage technology=covv_seq_technology zip=country date=covv_collection_date submission_date=covv_subm_date --tsv $(realpath !{metadata}) --db $db
• [x] ./sonar.py optimize --db ${db}
• [x] ./sonar.py info --db ${db}
• [x] ./sonar.py remove --db "\$db" --cpus "$task.cpus" --file "sequences-to-delete.ids"
• [x] ./sonar.py add --noprogress --db "\$db" --file "$day_fasta" --cpus $task.cpus --force
• [x] ./sonar.py update --db "\$db" --fields accession=taxon lineage=lineage --csv "${clades_pangolin}"
• [x] ./sonar.py match --ambig --tsv --db "\$db" | gzip > desh-covsonar-temp.tsv.gz
• [x] ./sonar.py update --db $rki_db --fields accession=IMS_ID zip=SENDING_LAB_PC lab=SENDING_LAB --tsv $desh_passed_meta
• [x] ./sonar.py match --db "$rki_db" --submission_date "${workflow.profile.contains('test') ? '2021-01-26' : params.date }" --tsv > "covsonar-match-yesterday.tsv"

vocal paper

• [x] python sonar.py match --lineage B.1.1.529 --lineage BA.% --with-sublineage --date 2021-12-01:2021-12-31 --db $db --tsv
• [x] python sonar.py match --lineage ^B.1.1.529 --lineage ^BA.% --date 2021-12-01:2021-12-31 --db $db --tsv

gisaid upload

• [x] {params.tool} add --db {output.db} -f {input.fasta} --cpus {threads} &> {log}
• [x] {params.tool} match --only_frameshifts --db {input.db} 1> {output} 2> {log}

interactive use

• [x] ?

[matthuska]

Closed due to stopped development on covsonar 2.