Update README.md and add more images of plugin in action

README.md

@@ -1,30 +1,46 @@
 # sublime-nextflow: [Nextflow] workflow completions, commands, syntax highlighting and snippets for [Sublime Text 4]
 
-- **WARNING:** Sublime Text 3 is no longer supported by this package. Only Sublime Text 4 is supported (requires Python 3.8 and new features in ST4).
-- **NOTE:** Only [DSL-2] Nextflow workflows are supported by this package.
+- **⚠️WARNING⚠️:** Sublime Text 3 is no longer supported by this package as of version 1.0.0. Only Sublime Text 4 is supported since this package requires Python 3.8 and new features in ST4.
+- **❗NOTE❗:** Only [DSL-2] Nextflow workflows are supported by this package. 
 
-This package provides [Nextflow]
+This package provides [Nextflow] workflow language:
 
 - completions (`params.`, `conda`, `<PROCESS>.out.<emit name>`)
-- commands (insert Biocontainer container directive, insert module import statement)
+- commands (insert container directive, insert module import statement)
 - syntax highlighting
 - snippets
 
-Basically a collection of things to make [Nextflow] workflow development a bit easier especially when trying to develop [nf-core] quality workflows.
+Essentially, this package tries to make [Nextflow] workflow development a bit easier especially when trying to develop [nf-core] conventions and best practices for developing [Nextflow] pipelines.
 
 ## Nextflow completions and commands
 
+### Process module include command
+
+- `ctrl+l,p` in an `.nf` file where you want to import your process
+
+![](images/include-process-command-quick-menu.png)
+
+- select the process you wish to import
+- something like the following will be inserted
+
+```nextflow
+include { MAKE_BED_MASK } from '../modules/local/make_bed_mask' addParams( options: modules['make_bed_mask'] )
+```
+
+The `addParams( options: modules['make_bed_mask'] )` may not be needed and can be removed; it assumes that you have a `conf/modules.config` with a map of your module `args`, `publish_dir`, etc (see [nf-core/modules](https://github.com/nf-core/modules#module-parameters) for more info).
 
 ### Workflow `params`
 
 **NOTE:** Completions and info popups for `params` depend on a valid `nextflow_schema.json` in your workflow root directory. Example [`nextflow_schema.json` for nf-core/viralrecon workflow](https://github.com/nf-core/viralrecon/blob/master/nextflow_schema.json).
 
 Navigate cursor to a `params.<variable>` to show a popup with info pulled from the `nextflow_schema.json` for that workflow parameter.
 
+![](images/params-popup-nf-core-viralrecon.png)
+
 
 ### [Conda] completion
 
-**NOTE:** [Conda] must be installed along with any channels (e.g. [bioconda], [conda-forge]) to get packages information
+**NOTE:** [Conda] must be installed along with any channels (e.g. [bioconda], [conda-forge]) to get packages information (needs to be able to run `conda search`).
 
 - Open the command palette (`ctrl+shift+p`) and run the `Nextflow: Fetch Conda packages information` command to fetch the latest Conda package info (runs `conda search`; may take a while).
 - In your process definition, inside the `conda` directive string press `ctrl+space` to bring up the completion list. *This may have a little delay since the package list may be very large.*
@@ -35,44 +51,79 @@ process PANGOLIN {
 }
 ```
 
-## [Biocontainer] insert command
+![](images/conda-completion.png)
+
+### Process output channel completion
+
+Get process named output (i.e. using the [`emit`](https://www.nextflow.io/docs/latest/dsl2.html#process-named-output) option) completions after typing `<PROCESS_NAME>.out.`.
+
+![](images/process-out-completion-nf-core-viralrecon.png)
 
-This command inserts similar code to what you'd find in an [nf-core modules](https://github.com/nf-core/modules) process definition with respect to process `container` directives. The container information is pulled from the [Singularity][] images [https://depot.galaxyproject.org/singularity/](https://depot.galaxyproject.org/singularity/) and cached. [Docker] container image tags point to the [Biocontainers][] [Quay.io page](https://quay.io/organization/biocontainers).
+- completion shows what's on the channel as well!
+
+### Container directive insert command
+
+This command inserts similar code to what you'd find in an [nf-core modules](https://github.com/nf-core/modules) process definition with respect to process `container` directives. The [Biocontainers] information is pulled from the [Singularity][] images [https://depot.galaxyproject.org/singularity/](https://depot.galaxyproject.org/singularity/) and cached as a Python pickle file. [Docker] container image tags point to the [Biocontainers][] [Quay.io page](https://quay.io/organization/biocontainers).
 
 - Open the command palette (`ctrl+shift+p`) and run the `Nextflow: Fetch Biocontainers information` command to fetch the latest [Biocontainers] list fetched from 
 - In your process definition, press `ctrl+l,c`, search for the container you're interested in
 
+![](images/container-command-quick-menu.png)
+
+- Select the program and version you're interested in to output the following:
+
 ```nextflow
-  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/pangolin:3.1.5--pyhdfd78af_0'
-  } else {
-    container 'quay.io/biocontainers/pangolin:3.1.5--pyhdfd78af_0'
-  }
+if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+  container 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--hdfd78af_1'
+} else {
+  container 'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1'
+}
 ```
 
 ## Nextflow Syntax Highlighting
 
 Nextflow syntax highlighting extends Sublime Text 4's Groovy syntax with highlighting of: 
 
 - imports (DSL-2 modules)
+  ![](images/syntax-highlighting-module-imports-nf-core-viralrecon.png)
 - workflow definitions
+  ![](images/syntax-highlighting-workflow-def-nf-core-viralrecon.png)
 - process definitions
+  ![](images/syntax-highlighting-process-def-nf-core-viralrecon.png)
 - channel highlighting based on matching `ch_*`
 - some invalid syntax checks (into channel in input tag and from channel in output tag)
 - highlighting special Nextflow functions and variables (`workflow`, `params`, `task`, etc)
 
+Process syntax highlighting and scoping allows one to easily go to the definition  or usages of a process (`ctrl+shift+g` keyboard shortcut):
+
+![](images/goto-process-definition.png)
+
 ## Nextflow Snippets
 
+Type one of the following and press `TAB`:
+
 - `!env`: `#!/usr/bin/env nextflow`
 - `proc`: [process](https://www.nextflow.io/docs/latest/process.html) snippet
-- `tag`: [tag](https://www.nextflow.io/docs/latest/process.html#tag) directive snippet
-- `pub`: [publishDir](https://www.nextflow.io/docs/latest/process.html#publishdir) directive snippet
+- `tag`: [tag](https://www.nextflow.io/docs/latest/process.html#tag) process directive snippet
+- `pub`: [publishDir](https://www.nextflow.io/docs/latest/process.html#publishdir) process directive snippet
 - `illumina`: Illumina paired-end reads file pairs channel
-- `cpus`: insert "${task.cpus}" into a script
+- `cpus`: insert `"${task.cpus}"` into a process script
 - `script_path`: specify user script (e.g. Python script) to use from `scripts/` directory in workflow base directory
 - `info`: `log.info` snippet 
 - `done`: on workflow complete or error message
 
+# Changelog
+
+## 1.0.0 - [2021-06-30]
+
+- Added syntax highlighting for Nextflow DSL-2
+- Added completions and commands for workflow `params`, `PROCESS.out.`, conda, container, module include
+- Removed some not very useful snippets
+
+## 0.1.0-alpha.1 - [2019-03-27]
+
+- Initial release with Groovy-based syntax highlighting and basic snippets
+
 [DSL-2]: https://www.nextflow.io/docs/latest/dsl2.html
 [Nextflow]: https://www.nextflow.io/
 [nf-core]: https://nf-co.re/
@@ -82,3 +133,10 @@ Nextflow syntax highlighting extends Sublime Text 4's Groovy syntax with highlig
 [Singularity]: https://sylabs.io/guides/3.7/user-guide/quick_start.html
 [Docker]: https://www.docker.com/
 [Sublime Text 4]: http://www.sublimetext.com/
+[Biocontainers]: https://biocontainers.pro/
+
+# License
+
+MIT License
+
+Copyright (c) Peter Kruczkiewicz