diff --git a/README.md b/README.md index dbebb478..ace8e8e3 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # miniwdl **[Workflow Description Language](http://openwdl.org/) static analysis toolkit for Python 3.6+** -![Project Status](https://img.shields.io/badge/status-prealpha-red.svg) +![Project Status](https://img.shields.io/badge/status-alpha-red.svg) [![PyPI version](https://img.shields.io/pypi/v/miniwdl.svg)](https://pypi.org/project/miniwdl/) [![MIT license](https://img.shields.io/badge/license-MIT-brightgreen.svg)](https://github.com/chanzuckerberg/miniwdl/blob/master/LICENSE) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black) @@ -10,7 +10,7 @@ *miniwdl* is a library for parsing WDL documents into a type-checked abstract syntax tree (AST), providing a foundation for new runtime systems, developer tooling, and language experimentation. It also includes a command-line tool which validates WDL documents and generates lint/style warnings. -This project in prealpha development; interfaces are liable to change substantially. +This project in alpha development; interfaces are liable to change somewhat. ## Installation @@ -32,7 +32,7 @@ $ miniwdl check --path skylab/library/tasks/ \ SmartSeq2SingleSample.wdl workflow SmartSeq2SingleCell - (Ln 14, Col 3) UnusedDeclaration, nothing references File gtf_file + (Ln 14, Col 8) UnusedDeclaration, nothing references File gtf_file call HISAT2.HISAT2PairedEnd call Picard.CollectMultipleMetrics call Picard.CollectRnaMetrics @@ -43,18 +43,31 @@ SmartSeq2SingleSample.wdl call ZarrUtils.SmartSeq2ZarrConversion GroupQCs : GroupMetricsOutputs.wdl task GroupQCOutputs - (Ln 10, Col 3) StringCoercion, String mem = :Int: - (Ln 11, Col 3) StringCoercion, String cpu = :Int: - (Ln 12, Col 3) StringCoercion, String disk_space = :Int: + (Ln 10, Col 10) StringCoercion, String mem = :Int: + (Ln 11, Col 10) StringCoercion, String cpu = :Int: + (Ln 12, Col 10) StringCoercion, String disk_space = :Int: HISAT2 : HISAT2.wdl task HISAT2PairedEnd task HISAT2RSEM task HISAT2InspectIndex (not called) task HISAT2SingleEnd (not called) - - ... + Picard : Picard.wdl + task CollectDuplicationMetrics + task CollectMultipleMetrics + task CollectRnaMetrics + RSEM : RSEM.wdl + task RSEMExpression + ZarrUtils : ZarrUtils.wdl + task SmartSeq2ZarrConversion + (Ln 36, Col 6) CommandShellCheck, SC2006 Use $(..) instead of legacy `..`. + (Ln 39, Col 9) CommandShellCheck, SC2006 Use $(..) instead of legacy `..`. + (Ln 39, Col 15) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting. + (Ln 40, Col 10) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting. + (Ln 40, Col 21) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting. ``` +In addition to its suite of WDL-specific warnings, `miniwdl check` uses [ShellCheck](https://www.shellcheck.net/), if available, to detect possible issues in each task command script. You may need to install ShellCheck separately, as it's not included with miniwdl. + If you haven't installed the PyPI package to get the `miniwdl` entry point, equivalently `python3 -m /path/to/miniwdl/WDL check ...`. ## `WDL` package