Merge branch 'blog-examples'

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

diff --git a/blog-examples/debugging/fastqc/fastqc_blog_broken.cwl b/blog-examples/debugging/fastqc/fastqc_blog_broken.cwl
new file mode 100644 (file)
index 0000000..8d3d348
--- /dev/null
+++ b/blog-examples/debugging/fastqc/fastqc_blog_broken.cwl
@@ -0,0 +1,53 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Quality check on FASTQ
+
+requirements:
+  DockerRequirement:
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.fastq1)
+      - $(inputs.fastq2)
+
+hints:
+  SoftwareRequirement:
+    packages:
+      FastQC:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
+        version: [ "0.11.9" ]
+
+inputs:
+  fastq1:
+    type: Files
+    label: One of set of pair-end FASTQs (R1)
+
+  fastq2:
+    type: File
+    label: One of set of pair-end FASTQs (R2)
+
+outputs:
+  out-html:
+    type: File[]
+    label: FASTQ QC reports
+    outputBinding:
+      glob: "*html"
+  out-zip:
+    type: File[]
+    label: Zip files of FASTQ QC report and associated data
+    outputBinding:
+      glob: "*fastqc.zip"
+
+baseCommand: fastqc
+
+arguments:
+  - "--noextract"
+  - $(inputs.fastq1.basename)
+  - $(inputs.fastq2.basename)
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial/blog-examples/debugging
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/