Add summary docs

src/SUMMARY.md

@@ -5,8 +5,8 @@
 
 # Commands
 
-- [nailpolish index](./generate-index.md)
-- [nailpolish summary](./summarize.md)
-- [nailpolish call](./call.md)
+- [nailpolish index](commands/generate-index.md)
+- [nailpolish summary](commands/summarize.md)
+- [nailpolish call](commands/call.md)
 
 # Reference

src/commands/call.md

@@ -0,0 +1,34 @@
+# nailpolish call
+
+Consensus call duplicated reads
+The reads must first have been [indexed](./generate-index.md).
+
+## Usage
+
+```shell
+$ nailpolish call --help
+Generate a consensus-called 'cleaned up' file
+
+Usage: nailpolish call [OPTIONS] --index <INDEX> --input <INPUT>
+
+Options:
+      --index <INDEX>          the index file
+      --input <INPUT>          the input .fastq
+      --output <OUTPUT>        the output .fasta; note that quality values are not preserved
+  -t, --threads <THREADS>      the number of threads to use [default: 4]
+  -d, --duplicates-only        only show the duplicated reads, not the single ones
+  -r, --report-original-reads  for each duplicate group of reads, report the original reads along with the consensus
+  -h, --help                   Print help
+```
+
+## Output format
+
+TODO
+
+## Options
+
+- `--duplicates-only`: By default, _nailpolish_ will consensus call all duplicated reads and also produces each
+  non-duplicated read intact. With this flag, only the duplicated reads will be produced, and all non-duplicated reads
+  will be skipped.
+- `--report-original-reads`: By default, when reads are consensus called, only the consensus read is produced.
+  With this flag, each of the original reads will be produced as well.

src/commands/summarize.md

@@ -0,0 +1,24 @@
+# nailpolish summary
+
+Quickly review the quality and duplicate rate of the dataset.
+The reads must first have been [indexed](./generate-index.md).
+
+## Usage
+
+```shell
+$ nailpolish summary --help
+Generate a summary of duplicate statistics from an index file
+
+Usage: nailpolish summary [OPTIONS] --index <INDEX>
+
+Options:
+      --index <INDEX>    the index file
+      --output <OUTPUT>  output file [default: summary.html]
+  -h, --help             Print help
+```
+
+## Output
+
+[See an example summary output file.](../assets/summary.html)
+
+<iframe src="../assets/summary.html" style="width: 100%; height: 60vh; min-height: 500px;"></iframe>

src/quickstart.md

@@ -27,7 +27,7 @@ wget https://github.com/DavidsonGroup/nailpolish/releases/download/sample-fastq-
 
 ## Indexation
 
-_For more information, see [nailpolish index](./generate-index.md)._
+_For more information, see [nailpolish index](commands/generate-index.md)._
 
 By default, nailpolish expects the barcode and UMI to be in the `@BC_UMI` format at the start of the header.
 Alternative barcode and UMI formats can be provided through either a preset (one of `bc-umi`, `umi-tools`, `illumina`)
@@ -40,7 +40,7 @@ nailpolish index --index index.tsv scmixology2_sample.fastq
 
 ## Summary of duplicate count
 
-_For more information, see [nailpolish summary](./summarize.md)._
+_For more information, see [nailpolish summary](commands/summarize.md)._
 
 A .html file can be generated to summarise some key statistics about the input reads.
 The output file is written to `summary.html` by default.
@@ -53,7 +53,7 @@ nailpolish summary index.tsv
 
 ## Consensus call duplicates
 
-_For more information, see [nailpolish call](./call.md)._
+_For more information, see [nailpolish call](commands/call.md)._
 
 By consensus calling duplicates, only one read is returned per UMI group.
 For singleton reads, there is no change
@@ -68,4 +68,4 @@ nailpolish call \
 ```
 
 There are alternative parameters which can be passed to configure the output.
-See the _[nailpolish call](./call.md)_ documentation for more.
+See the _[nailpolish call](commands/call.md)_ documentation for more.