Add README.md and other details (#5)

* Update README.md

* Update pyproject.toml

* Update .bumpversion.cfg

Author: scwatts

.bumpversion.cfg

@@ -7,3 +7,7 @@ parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[a-z0-9+]+)
 [bumpversion:file:pyproject.toml]
 search = version = "{current_version}"
 replace = version = "{new_version}"
+
+[bumpversion:file:README.md]
+search = bolt:{current_version}
+replace = bolt:{new_version}

README.md

@@ -1 +1,75 @@
 # bolt
+
+`bolt` implements the UMCCR WGS post-processing logic and supporting functionality, and is used extensively throughout the
+UMCCR workflow [`sash`](https://github.com/scwatts/sash).
+
+The post-processing logic is organised into individual processing steps, which are collectively grouped according to the
+type of data processed. Each processing step is accessible through specific `bolt` commands (see [Available
+commands](#available-commands) for the complete listing) and can be run in isolation. Processing steps are integrated
+into a production workflow in the `sash` pipeline.
+
+## Table of contents
+
+* [Available commands](#available-commands)
+* [Docker images](#docker-images)
+* [Usage](#usage)
+
+## Available commands
+
+### Germline small variants
+
+| Command                      | Purpose                                     |
+| ---                          | ---                                         |
+| `bolt smlv_germline prepare` | Select variants given a genome regions file |
+| `bolt smlv_germline report`  | Generate summary statistics and CPSR report |
+
+### Somatic small variants
+
+| Command                      | Purpose                                                       |
+| ---                          | ---                                                           |
+| `bolt smlv_somatic rescue`   | Supplement DRAGEN calls with SAGE calls and info              |
+| `bolt smlv_somatic annotate` | Annotate variants with PCGR, PON, and defined genomic regions |
+| `bolt smlv_somatic filter`   | Set and apply filters for variants                            |
+| `bolt smlv_somatic report`   | Generate summary statistics and PCGR report                   |
+
+### Somatic structural variants
+
+| Command                      | Purpose                                                      |
+| ---                          | ---                                                          |
+| `bolt sv_somatic annotate`   | Annotate SVs (and CNVs) with SnpEff                          |
+| `bolt sv_somatic prioritise` | Prioritise variants with rank ordering using `prioritize_sv` |
+
+### Other
+
+| Command                      | Purpose                                                 |
+| ---                          | ---                                                     |
+| `bolt other cancer_report`   | Generate the UMCCR Cancer Report                        |
+| `bolt other multiqc_report`  | Generate the MultiQC report                             |
+| `bolt other purple_baf_plot` | Create a modified PURPLE plot with β-allele frequencies |
+
+## Docker images
+
+For convenience, several Docker images are provided to run `bolt` aimed at balancing image size with the complexity of
+the software environment and dependencies. Consequently, dependencies are split across six images:
+
+| Name    | Docker image URI                    | Commands                       |
+| ---     | ---                                 | ---                            |
+| pcgr    | ghcr.io/scwatts/bolt:0.2.13-pcgr    | • `bolt smlv_germline report`<br />• `bolt smlv_somatic annotate`<br />• `bolt smlv_somatic report`<br /> |
+| gpgr    | ghcr.io/scwatts/bolt:0.2.13-gpgr    | • `bolt other cancer_report`   |
+| snpeff  | ghcr.io/scwatts/bolt:0.2.13-snpeff  | • `bolt sv_somatic annotate`   |
+| circos  | ghcr.io/scwatts/bolt:0.2.13-circos  | • `bolt other purple_baf_plot` |
+| multiqc | ghcr.io/scwatts/bolt:0.2.13-multiqc | • `bolt other multiqc_report`  |
+| base    | ghcr.io/scwatts/bolt:0.2.13         | • `bolt smlv_germline prepare`<br />• `bolt smlv_somatic rescue`<br />• `bolt smlv_somatic filter`<br />• `bolt sv_somatic prioritise`<br /> |
+
+## Usage
+
+Given the nature of software dependencies required, it is strongly recommended to run `bolt` commands via the existing
+[Docker images](#docker-images):
+
+```bash
+docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/scwatts/bolt:0.2.13 \
+  bolt smlv_somatic filter \
+    --tumor_name tumor_sample \
+    --vcf_fp tumor_sample.vcf.gz \
+    --output_dir ./
+```

pyproject.toml

@@ -9,6 +9,9 @@ include = ["bolt*"]
 [project]
 name = "bolt"
 version = "0.2.13"
+authors = [
+  {name = "Stephen Watts", email = "stephen.watts@umccr.org"},
+]
 dependencies = [
     "biopython",
     "cyvcf2",