seqera 0.4.0 → 0.5.0

package/README.md

@@ -0,0 +1,326 @@
+# Seqera AI CLI
+
+AI-powered assistant for bioinformatics workflows and [Seqera Platform](https://seqera.io).
+
+> **Beta:** Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.
+
+> **Note:** Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
+
+## Get started
+
+1. Install the Seqera AI CLI:
+
+    ```bash
+    pip install seqera
+    ```
+
+    See [Installation](https://docs.seqera.io/platform-cloud/seqera-ai/installation) for a comprehensive installation guide.
+
+2. Log in to your Seqera account:
+
+    ```bash
+    seqera login
+    ```
+
+    See [Authentication](https://docs.seqera.io/platform-cloud/seqera-ai/authentication) for a comprehensive authentication guide.
+
+3. Start Seqera AI:
+
+    ```bash
+    seqera ai
+    ```
+
+4. Run your first prompt:
+
+    ```
+    /debug
+    ```
+
+    See [Use cases](https://docs.seqera.io/platform-cloud/seqera-ai/use-cases) for a comprehensive list of use cases.
+
+## Use cases
+
+Seqera AI is an intelligent command-line assistant that helps you build, run, and manage bioinformatics workflows. The following sections describe several common use cases.
+
+### Work with Nextflow
+
+Seqera AI helps you develop, debug, and understand Nextflow pipelines with AI-powered analysis and code generation.
+
+![Use Seqera AI CLI to debug Nextflow pipeline scripts](https://docs.seqera.io/assets/images/pipeline-debug-375acd53dafcfc2ac1fed24125f1bdb6.gif)
+
+<details open>
+<summary><strong>Working with Nextflow</strong></summary>
+
+**Understand your pipeline structure**:
+
+```
+> Show me the structure of main.nf
+```
+
+```
+> What processes are defined in this pipeline?
+```
+
+**Generate a `nextflow.config` file**:
+
+```
+> /config
+```
+
+**Debug your pipeline**:
+
+```
+> /debug
+```
+
+```
+> Why is my pipeline failing?
+```
+
+**Generate a schema (`nextflow_schema.json`) file**:
+
+```
+> /schema
+```
+
+**Convert scripts to Nextflow**:
+
+```
+> /convert-python-script
+```
+
+</details>
+
+### Build containers with Wave
+
+Seqera AI can create containerized environments using Wave, without requiring you to write Dockerfiles.
+
+![Use Seqera AI CLI to build containers with Wave](https://docs.seqera.io/assets/images/building-wave-container-69b634e33c69b0d3a2e09521108a5ad3.gif)
+
+<details open>
+<summary><strong>Building containers with Wave</strong></summary>
+
+**Create a container with conda packages**:
+
+```
+> Create a container with samtools and bwa from bioconda
+```
+
+**Create a container with pip packages**:
+
+```
+> Build a container with pandas, numpy, and scikit-learn
+```
+
+**Get a container for a specific tool**:
+
+```
+> I need a container with FastQC version 0.12.1
+```
+
+> **Note:** The assistant will generate a Wave container URL that you can use directly in your Nextflow pipelines or pull with Docker.
+
+</details>
+
+### Customize your session
+
+Customize your session with command-line options.
+
+<details open>
+<summary><strong>Customize your session</strong></summary>
+
+**Start in a specific directory**:
+
+```bash
+seqera ai -w /path/to/project
+```
+
+**Set approval mode for local commands**:
+
+```bash
+seqera ai -a full
+```
+
+</details>
+
+### Exit the assistant
+
+End your Seqera AI session when done.
+
+<details open>
+<summary><strong>Exit the assistant</strong></summary>
+
+**To end your session**:
+
+- Type `exit` or `quit`
+- Press `Ctrl+C`
+
+> **Note:** Your conversation history is preserved for the session but not stored permanently.
+
+</details>
+
+### Use slash commands
+
+Seqera AI includes built-in slash commands for common workflows.
+
+<details open>
+<summary><strong>Use slash commands</strong></summary>
+
+**Type `/` to see all available commands**:
+
+| Command | Description |
+|---------|-------------|
+| `/config` | Generate a nextflow.config file |
+| `/schema` | Generate a Nextflow schema |
+| `/debug` | Run nextflow lint and preview |
+| `/debug-last-run` | Debug the last local run |
+| `/debug-last-run-on-seqera` | Debug the last Platform run |
+| `/migrate-from-wdl` | Convert WDL to Nextflow |
+| `/migrate-from-snakemake` | Convert Snakemake to Nextflow |
+| `/convert-python-script` | Convert Python script to Nextflow |
+| `/convert-r-script` | Convert R script to Nextflow |
+| `/convert-jupyter-notebook` | Convert Jupyter notebook to Nextflow |
+| `/write-nf-test` | Write nf-tests for your pipeline |
+
+</details>
+
+### Work with data
+
+Seqera AI helps you manage data through Platform data links and access reference datasets.
+
+<details open>
+<summary><strong>Working with data</strong></summary>
+
+**Browse data links**:
+
+```
+> List my data links
+```
+
+```
+> Show me the contents of my S3 data link
+```
+
+**Download and upload files**:
+
+```
+> Generate a download URL for results/final_report.html
+```
+
+```
+> Upload my local results to the data link
+```
+
+**Access reference data**:
+
+```
+> Find the human reference genome GRCh38
+```
+
+```
+> Search for RNA-Seq test data
+```
+
+</details>
+
+### Work with local files
+
+Seqera AI can interact with files in your current working directory.
+
+<details open>
+<summary><strong>Work with local files</strong></summary>
+
+**Start the assistant from your project folder**:
+
+```bash
+cd /path/to/your/project
+seqera ai
+```
+
+**Then, ask the assistant to help with local tasks**:
+
+```
+> Show me the structure of main.nf
+```
+
+```
+> Add a new process to handle quality control
+```
+
+> **Note:** Local file operations are controlled by [approval modes](https://docs.seqera.io/platform-cloud/seqera-ai/command-approval). By default, the assistant will ask for your approval before making changes outside your working directory or running potentially dangerous commands.
+
+</details>
+
+### Work with nf-core modules
+
+Seqera AI provides access to over 1,000 nf-core modules for common bioinformatics tasks.
+
+<details open>
+<summary><strong>Working with nf-core modules</strong></summary>
+
+**Search for modules**:
+
+```
+> Find nf-core modules for sequence alignment
+```
+
+```
+> What modules are available for variant calling?
+```
+
+**Get module details**:
+
+```
+> Show me how to use the nf-core/bwa/mem module
+```
+
+**Run a module**:
+
+```
+> Run FastQC on my FASTQ files
+```
+
+> **Note:** The assistant can generate the exact Nextflow command with proper parameters for your data.
+
+</details>
+
+### Work with Seqera Platform
+
+Use Seqera Platform capabilities to run and manage workflows at scale with AI assistance.
+
+![Use Seqera AI CLI to debug Platform run errors](https://docs.seqera.io/assets/images/sp-run-debug-233344952c4c20cc5da357003c0fe2d9.gif)
+
+<details open>
+<summary><strong>Working with Seqera Platform</strong></summary>
+
+**List your workflows**:
+
+```
+> List my recent workflows
+```
+
+**Launch a pipeline**:
+
+```
+> Launch the nf-core/rnaseq pipeline with the test profile
+```
+
+**Debug failed runs**:
+
+```
+> Why did my last workflow fail?
+```
+
+```
+> Get the logs for the failed task in my last run
+```
+
+</details>
+
+## Learn more
+
+- [Installation](https://docs.seqera.io/platform-cloud/seqera-ai/installation): Detailed installation instructions
+- [Authentication](https://docs.seqera.io/platform-cloud/seqera-ai/authentication): Log in, log out, and session management
+- [Command approval](https://docs.seqera.io/platform-cloud/seqera-ai/command-approval): Control which commands run automatically
+- [Use cases](https://docs.seqera.io/platform-cloud/seqera-ai/use-cases): Seqera AI CLI use cases
+- [Troubleshooting](https://docs.seqera.io/platform-cloud/troubleshooting_and_faqs/seqera-ai): Troubleshoot common errors

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "seqera",
-  "version": "0.4.0",
+  "version": "0.5.0",
   "description": "AI-powered CLI for Seqera Platform - bioinformatics workflow management",
   "keywords": [
     "seqera",
@@ -11,17 +11,18 @@
     "cli"
   ],
   "author": "Seqera Labs",
-  "license": "Apache-2.0",
+  "license": "Custom",
   "bin": {
     "seqera": "bin/seqera"
   },
   "files": [
-    "bin/**"
+    "bin/**",
+    "README.md"
   ],
   "optionalDependencies": {
-    "@seqera/cli-darwin-arm64": "0.4.0",
-    "@seqera/cli-darwin-x64": "0.4.0",
-    "@seqera/cli-linux-x64": "0.4.0"
+    "@seqera/cli-darwin-arm64": "0.5.0",
+    "@seqera/cli-darwin-x64": "0.5.0",
+    "@seqera/cli-linux-x64": "0.5.0"
   },
   "engines": {
     "node": ">=18"