X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/1ab06313ca284ff3c75e0a086ce2c89af0fefa6d..e45856f97fb592f4deb3821a16d0c5be0b6ccf44:/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl b/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl
new file mode 100644
index 0000000..84b9c40
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+++ b/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl
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+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: File
+    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/