Fix profiles - Githubissues

czbiohub-sf / sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

GNU Affero General Public License v3.0

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Closed samlhao closed 4 years ago

samlhao commented 4 years ago

The files are named ambiguously, so I added two profiles to run the consensus calling more clearly, e.g. -profile artic,awsbatch or -profiles msspe,awsbatch.
removed references to old nextstrain steps
removed unused scripts

samlhao commented 4 years ago

Good point, I'll have this PR cover a general "fix profiles" purpose