From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 2 Jul 2020 14:50:54 +0000 (+0000)
Subject: Updating for new Docker containter
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/56ae937c2f96a4ecc3f35f932d4e2246d76db309

Updating for new Docker containter
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/cwl/helper/fastqc.cwl b/WGS-processing/cwl/helper/fastqc.cwl
index 852c82b..fffcdad 100644
--- a/WGS-processing/cwl/helper/fastqc.cwl
+++ b/WGS-processing/cwl/helper/fastqc.cwl
@@ -4,11 +4,7 @@ label: Quality check on FASTQ
 
 requirements:
   DockerRequirement:
-    dockerPull: curii/fastqc
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.fastq1)
-      - $(inputs.fastq2)
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
 
 hints:
   SoftwareRequirement:
@@ -40,12 +36,11 @@ outputs:
     outputBinding:
       glob: "*fastqc.zip"
 
-baseCommand: perl
+baseCommand: fastqc 
 
 arguments:
-  - /FastQC/fastqc
-  - $(inputs.fastq1.basename)
-  - $(inputs.fastq2.basename)
+  - $(inputs.fastq1.path)
+  - $(inputs.fastq2.path)
 
 s:codeRepository: https://github.com/arvados/arvados-tutorial
 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
@@ -54,6 +49,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl