Updating fastq

[arvados-tutorial.git] / blog-examples / debugging / fastq_example / fastqc_blog_broken.cwl

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl b/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl
new file mode 100644 (file)
index 0000000..8171be3
--- /dev/null
+++ b/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Quality check on FASTQ
+
+requirements:
+  DockerRequirement:
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
+
+inputs:
+  fastq1:
+    type: Files 
+  fastq2:
+    type: File
+
+outputs:
+  out-html:
+    type: File
+    outputBinding:
+      glob: "*html"
+  out-zip:
+    type: File[]
+    outputBinding:
+      glob: "*fastqc.zip"
+
+baseCommand: fastqc
+
+arguments:
+  - $(inputs.fastq1.path)
+  - $(inputs.fastq2.path)