Merge pull request #90 from antgonza/improve-README

improve README

Author: charles-cowart

README.rst

@@ -1,10 +1,23 @@
-# qp-knight-lab-processing
-
 |Build Status| |Coverage Status|
 
-General Knight Lab Admin Commands for sequence processing in Qiita.
+Knight Lab Admin Commands for Qiita. This is an Admin only plugin.
+
+This plugin provides the following commands:
+
+#. Sequence Processing Pipeline (SPP):
+
+This command converts the BCL to FASTQ files, does adaptor and host/human sequence filtering, summarizes results and uploads the resulting files to Qiita as one or more new preparations and artifacts. This command is based on [mg-scripts](https://github.com/biocore/mg-scripts) and (metapool)[https://github.com/biocore/metagenomics_pooling_notebook/].
+
+The new preparations that the SPP adds contain some automatically generated extra columns:
+
+* raw_reads_r1r2: this is the total number of reads that the sequencing generated for R1 and R2.
+
+* total_biological_reads_r1r2: the total of reads minus the adapters but before host/human filtering for R1 and R2.
+
+* quality_filtered_reads_r1r2: total of reads that passed host/human filtering for R1 and R2.
+
+* fraction_passing_quality_filter: the fraction of reads that are in quality_filtered_reads_r1r2 from the raw_reads_r1r2.
 
-This is an Admin only plugin
 
 .. |Build Status| image:: https://github.com/qiita-spots/qp-knight-lab-processing/actions/workflows/qiita-plugin-ci.yml/badge.svg
    :target: https://github.com/qiita-spots/qp-knight-lab-processing/actions/workflows/qiita-plugin-ci.yml