Update README.md

chanzuckerberg · Jan 25, 2019 · e24aaec · e24aaec
1 parent fa8d382
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Showing 1 changed file with 21 additions and 8 deletions.
diff --git 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