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microbiomeDB/amplicon_sequencing
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In this directory are subdirectories for amplicon sequencing studies. Each study/ subdirectory needs: 1. a samplesheet.csv file w 2-4 columns `sampleID`,`forwardReads`,`reverseReads`,`run` 2. a nf-params.json file w configuration for how airflow + nf-core should run 3. fastq.gz files There is also a file `amplicon_studies.csv` with two columns `studyName` and `studyPath`. When you have made your subdirectory for your study and are happy w it, you should add a row to this csv file. Eventually, modifications to this file trigger an Airflow run for the associated nf-core/ampliseq DAG. For now, trigger it manually. IMPORTANT NOTES: - It is best practice to include full (as opposed to relative) paths where they are needed - An example directory exists called test_study - There is a file called processed_studies_provenance.csv. Mostly you should NOT touch this.* * Possible exception being to remove a study to force it to re-run next time amplicon_studies.csv were touched.
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A collection of amplicon sequencing data sets intended for use with the mbio-airflow-dags repository
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