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README.md

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 # aladdin-miqScore16S
-Nextflow pipeline that calculates MIQ 16S score. Compatible with Aladdin platform
+Nextflow pipeline that calculates 16S MIQ score. Compatible with Compatible with [Aladdin Bioinformatics Platform](https://www.aladdin101.org/).. This is essentially a Nextflow wrapper that runs the code at [miqScore16SPublic](https://github.com/Zymo-Research/miqScore16SPublic) repo. Please refer to the original repo for more information on the source code.
+
+## Adaptation for Aladdin
+In order to be compatible with Aladdin platform, this pipeline requires a design CSV file as input. The design CSV file must have the following format
+```
+group,sample,read_1,read_2
+,Sample1,s3://mybucket/this_is_s1_R1.fastq.gz,s3://mybucket/this_is_s1_R2.fastq.gz
+```
+Because the [miqScore16SPublic](https://github.com/Zymo-Research/miqScore16SPublic) code only supports one sample at a time, only the 1st row after the header is recognized.
+
+## How to run the pipeline
+
+### Prerequisites
+* [Nextflow](https://www.nextflow.io) version 20.07.1 or later
+* [Docker](https://www.docker.com/) if using `docker` profile
+* Permissions to AWS S3 and Batch resources if using `awsbacth` profile
+
+### Using Docker
+```bash
+nextflow run Zymo-Research/aladdin-miqScore16S \
+	--profile docker \
+	--design "<path to design CSV file>"
+```
+
+### Using AWS Batch
+```bash
+nextflow run Zymo-Research/aladdin-miqScore16S \
+	-profile awsbatch \
+	--design "<path to design CSV file>" \
+	-work-dir "<work dir on S3>" \
+	--awsqueue "<SQS ARN>" \
+	--outdir "<output dir on S3>" \
+```
+The parameters `--awsqueue`, `-work-dir`, and `--outdir` are required when running on AWS Batch, the latter two must be directories on S3.
+
+## Report and Documentation
+
+#### Sample report
+A sample report this pipeline produces can be found [here](https://zymo-research.github.io/pipeline-resources/reports/MIQscore_16S_sample_report.html).
+
+#### Report documentation
+A documentation explaining how to understand the report can be found [here](https://zymo-research.github.io/pipeline-resources/report_docs/MIQscore_documentation.html).